annovar: tools/tools/annovar/annovar.sh annotate

annotate tools/tools/annovar/annovar.sh @ 5:4600be69b96f draft

Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03

author	saskia-hiltemann
date	Thu, 01 Oct 2015 04:24:45 -0400
parents
children

rev	line source
5 4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1 #!/bin/bash
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	3 test="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	4 dofilter="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	5
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	6 #########################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	7 # DEFINE SOME
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	8 # FUNCTIONS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	9 #########################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	10
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	11 function usage(){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	12 echo "usage: $0 todo"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	13 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	14
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	15 function runfilter(){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	16 ifile=$1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	17 columnname=$2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	18 threshold=$3
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	19
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	20 if [[ $threshold == "-1" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	21 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	22 echo "not filtering"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	23 return
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	24 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	25
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	26 echo "filtering: $columnname, $threshold"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	27 cat $ifile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	28
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	29 #get column number corresponding to column header
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	30 column=`awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	31 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	32 col=-1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	33 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	34 if(FNR==1){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	35 for(i=1;i<=NF;i++){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	36 if($i == "'"${columnname}"'")
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	37 col=i
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	38 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	39 print col
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	40 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	41 }' $ifile `
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	42
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	43 if [ $column == -1 ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	44 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	45 echo "no such column, exiting"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	46 return
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	47 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	48
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	49 #perform filtering using the threshold
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	50 awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	51 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	52 OFS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	53 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	54 if(FNR==1)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	55 print $0;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	56 if(FNR>1){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	57 if( $"'"${column}"'" == "" ) # empty column, then print
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	58 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	59 else if ("'"${threshold}"'" == "text"){} #if set to text dont check threshold
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	60
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	61 else if ($"'"${column}"'" < "'"${threshold}"'") #else do check it
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	62 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	63 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	64 }' $ifile > tmpfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	65
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	66 mv tmpfile $ifile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	67 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	68
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	69 # arguments: originalfile,resultfile,chrcol,startcol,endcol,refcol,obscol,addcols
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	70 function joinresults(){
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	71 ofile=$1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	72 rfile=$2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	73 colchr=$3
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	74 colstart=$4
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	75 colend=$5
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	76 colref=$6
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	77 colobs=$7
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	78 addcols=$8 #e.g. "B.col1,B.col2"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	79
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	80 test="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	81
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	82 # echo "joining result with original file"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	83 if [ $test == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	84 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	85 echo "ofile: $ofile"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	86 head $ofile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	87 echo "rfile: $rfile"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	88 head $rfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	89 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	90 numlines=`wc $rfile \| cut -d" " -f2`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	91
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	92 # if empty results file, just add header fields
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	93 if [[ ! -s $rfile ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	94 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	95 dummycol=${addcols:2}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	96 outputcol=${dummycol//",B."/" "}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	97 numcommas=`echo "$addcols" \| grep -o "," \| wc -l`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	98
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	99 awk 'BEGIN{FS="\t";OFS="\t"}{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	100 if(FNR==1)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	101 print $0,"'"$outputcol"'";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	102 else{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	103 printf $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	104 for(i=0;i<="'"$numcommas"'"+1;i++)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	105 printf "\t"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	106 printf "\n"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	107 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	108 }END{}' $ofile > tempofile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	109
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	110 mv tempofile $ofile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	111 return
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	112 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	113
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	114
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	115 #get input file column names for cgatools join
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	116 col_chr_name=`head -1 $rfile \| cut -f${colchr}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	117 col_start_name=`head -1 $rfile \| cut -f${colstart}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	118 col_end_name=`head -1 $rfile \| cut -f${colend}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	119 col_ref_name=`head -1 $rfile \| cut -f${colref}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	120 col_obs_name=`head -1 $rfile \| cut -f${colobs}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	121
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	122 #get annotation file column names for cgatools join
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	123 chr_name=`head -1 $ofile \| cut -f${chrcol}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	124 start_name=`head -1 $ofile \| cut -f${startcol}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	125 end_name=`head -1 $ofile \| cut -f${endcol}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	126 ref_name=`head -1 $ofile \| cut -f${refcol}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	127 obs_name=`head -1 $ofile \| cut -f${obscol}`
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	128
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	129 if [ $test == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	130 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	131 echo "input file"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	132 echo "chr col: $col_chr_name ($colchr)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	133 echo "start col: $col_start_name ($colstart)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	134 echo "end col: $col_end_name ($colend)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	135 echo "ref col: $col_ref_name ($colref)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	136 echo "obs col: $col_obs_name ($colobs)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	137 echo ""
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	138 echo "annotation file"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	139 echo "chr col: $chr_name ($chrcol)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	140 echo "start col: $start_name ($startcol)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	141 echo "end col: $end_name ($endcol)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	142 echo "ref col: $ref_name ($refcol)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	143 echo "obs col: $obs_name ($obscol)"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	144 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	145
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	146 #perform join
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	147 cgatools join --beta \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	148 --input $ofile $rfile \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	149 --output temporiginal \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	150 --match ${chr_name}:${col_chr_name} \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	151 --match ${start_name}:${col_start_name} \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	152 --match ${end_name}:${col_end_name} \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	153 --match ${ref_name}:${col_ref_name} \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	154 --match ${obs_name}:${col_obs_name} \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	155 --select A.*,$addcols \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	156 --always-dump \
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	157 --output-mode compact
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	158
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	159 #replace originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	160 sed -i 's/^>//g' temporiginal #join sometimes adds a '>' symbol to header
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	161 mv temporiginal originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	162
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	163 if [ $test == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	164 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	165 echo "joining complete"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	166 head originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	167 echo ""
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	168 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	169
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	170 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	171
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	172
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	173
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	174
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	175 #################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	176 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	177 # PARSE PARAMETERS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	178 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	179 #################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	180
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	181
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	182 set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` \|\| usage
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	183 [ $# -eq 0 ] && usage
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	184
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	185
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	186
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	187 while [ $# -gt 0 ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	188 do
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	189 case "$1" in
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	190 --inputfile) infile=$2;shift;; # inputfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	191 --buildver) buildvertmp=$2;shift;; # hg18 or hg19
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	192 --humandb) humandbtmp=$2;shift;; # location of humandb database
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	193 --varfile) varfile=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	194 --VCF) vcf=$2;shift;; #Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	195 --chrcol) chrcol=$2;shift;; # which column has chr
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	196 --startcol) startcol=$2;shift;; # which column has start
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	197 --endcol) endcol=$2;shift;; # which column has end
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	198 --refcol) refcol=$2;shift;; # which column has ref
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	199 --obscol) obscol=$2;shift;; # which column has alt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	200 --vartypecol) vartypecol=$2;shift;; # which column has vartype
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	201 --convertcoords) convertcoords=$2;shift;; # Y or N convert coordinate from CG to 1-based?
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	202 --geneanno) geneanno=$2;shift;; # comma-separated list of strings refSeq, knowngene, ensgene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	203 --hgvs) hgvs=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	204 --verdbsnp) verdbsnp=$2;shift;; #comma-separated list of dbsnp version to annotate with (e.g. "132,135NonFlagged,137,138")"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	205 --tfbs) tfbs=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	206 --mce) mce=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	207 --cytoband) cytoband=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	208 --segdup) segdup=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	209 --dgv) dgv=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	210 --gwas) gwas=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	211 --ver1000g) ver1000g=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	212 --cg46) cg46=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	213 --cg69) cg69=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	214 --impactscores) impactscores=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	215 --newimpactscores) newimpactscores=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	216 --otherinfo) otherinfo=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	217 --scriptsdir) scriptsdirtmp=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	218 --esp) esp=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	219 --exac03) exac03=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	220 --gerp) gerp=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	221 --cosmic61) cosmic61=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	222 --cosmic63) cosmic63=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	223 --cosmic64) cosmic64=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	224 --cosmic65) cosmic65=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	225 --cosmic67) cosmic67=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	226 --cosmic68) cosmic68=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	227 --nci60) nci60=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	228 --clinvar) clinvar=$2;shift;; # Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	229 --filt_dbsnp) filt_dbsnp=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	230 --filt1000GALL) threshold_1000g_ALL=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	231 --filt1000GAFR) threshold_1000g_AFR=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	232 --filt1000GAMR) threshold_1000g_AMR=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	233 --filt1000GASN) threshold_1000g_ASN=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	234 --filt1000GEUR) threshold_1000g_EUR=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	235 --filtESP6500ALL) threshold_ESP6500_ALL=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	236 --filtESP6500EA) threshold_ESP6500_EA=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	237 --filtESP6500AA) threshold_ESP6500_AA=$2;shift;; #threshold value
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	238 --filtcg46) threshold_cg46=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	239 --filtcg69) threshold_cg69=$2;shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	240 --outall) outfile_all=$2;shift;; # file
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	241 --outfilt) outfile_filt=$2;shift;; # file
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	242 --outinvalid) outfile_invalid=$2;shift;; #file
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	243 --dorunannovar) dorunannovar=$2;shift;; #Y or N
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	244 -h) shift;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	245 --) shift;break;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	246 -*) usage;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	247 *) break;;
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	248 esac
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	249 shift
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	250 done
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	251
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	252 #sometimes galaxy screws up these variables after updates, if comma-separated list, use only what is before first comma
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	253 humandb=${humandbtmp%,*}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	254 buildver=${buildvertmp%,*}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	255 scriptsdir=${scriptsdirtmp%,*}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	256
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	257
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	258 if [ $test == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	259 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	260 echo "dorunannovar: $dorunannovar"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	261 echo "infile: $infile"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	262 echo "buildver: $buildver"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	263 echo "annovardb: $humandb"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	264 echo "verdbnsp: $verdbsnp"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	265 echo "geneanno: $geneanno"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	266 echo "tfbs: $tfbs"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	267 echo "mce: $mce"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	268 echo "cytoband: $cytoband"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	269 echo "segdup: $segdup"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	270 echo "dgv: $dgv"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	271 echo "gwas: $gwas"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	272 echo "g1000: ${g1000}"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	273 echo "cg46: ${cg46}"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	274 echo "cg69: ${cg69}"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	275 echo "impactscores: $impactscores"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	276 echo "impactscores: $newimpactscores"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	277 echo "esp: $esp"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	278 echo "gerp: $gerp"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	279 echo "cosmic: $cosmic"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	280 echo "outfile: $outfile_all"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	281 echo "outinvalid: $outfile_invalid"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	282 echo "outfiltered: $outfile_filt"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	283 echo "varfile: $varfile"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	284 echo "vcf" $vcf
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	285 echo "chrcol: $chrcol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	286 echo "startcol: $startcol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	287 echo "endcol: $endcol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	288 echo "refcol: $refcol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	289 echo "obscol: $obscol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	290 echo "convertcoords: $convertcoords"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	291 echo "vartypecol: $vartypecol"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	292 echo "dofilter: $dofilter"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	293 echo "threshold_1000g_ALL : $threshold_1000g_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	294 echo "threshold_1000g_AFR : $threshold_1000g_AFR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	295 echo "threshold_1000g_AMR : $threshold_1000g_AMR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	296 echo "threshold_1000g_ASN : $threshold_1000g_ASN"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	297 echo "threshold_1000g_EUR : $threshold_1000g_EUR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	298 echo "threshold_ESP6500_ALL: $threshold_ESP6500_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	299 echo "threshold_ESP6500_EA : $threshold_ESP6500_EA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	300 echo "threshold_ESP6500_AA : $threshold_ESP6500_AA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	301
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	302 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	303
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	304
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	305
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	306 ############################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	307 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	308 # Annotate Variants
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	309 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	310 ############################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	311
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	312 #parse geneanno param
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	313 refgene="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	314 knowngene="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	315 ensgene="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	316
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	317 if [[ $geneanno =~ "refSeq" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	318 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	319 refgene="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	320 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	321 if [[ $geneanno =~ "knowngene" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	322 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	323 knowngene="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	324 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	325 if [[ $geneanno =~ "ensgene" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	326 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	327 ensgene="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	328 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	329 if [ $hgvs == "N" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	330 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	331 hgvs=""
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	332 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	333
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	334 #parse verdbsnp/1000g/esp strings
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	335 dbsnpstr=${verdbsnp//,/ }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	336 filt_dbsnpstr=${filt_dbsnp//,/ }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	337 g1000str=${ver1000g//,/ }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	338 espstr=${esp//,/ }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	339
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	340 if [ $test == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	341 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	342 echo "annotate dbsnp: $dbsnpstr"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	343 echo "annotate esp: $espstr"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	344 echo "filter dbsnp: $filt_dbsnpstr"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	345 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	346
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	347 mutationtaster="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	348 avsift="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	349 lrt="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	350 polyphen2="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	351 phylop="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	352 ljbsift="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	353
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	354 #parse old impactscores param (obsolete)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	355 if [[ $impactscores =~ "mutationtaster" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	356 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	357 mutationtaster="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	358 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	359 if [[ $impactscores =~ "sift" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	360 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	361 avsift="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	362 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	363 if [[ $impactscores =~ "lrt" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	364 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	365 lrt="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	366 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	367 if [[ $impactscores =~ "ljbsift" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	368 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	369 ljbsift="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	370 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	371 if [[ $impactscores =~ "ljb2sift" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	372 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	373 ljb2sift="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	374 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	375 if [[ $impactscores =~ "pp2" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	376 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	377 polyphen2="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	378 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	379 if [[ $impactscores =~ "phylop" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	380 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	381 phylop="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	382 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	383
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	384 if [[ $varfile == "Y" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	385 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	386 convertcoords="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	387 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	388
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	389 #ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	390
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	391 ljb2_sift="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	392 ljb2_pp2hdiv="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	393 ljb2_pp2hvar="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	394 ljb2_lrt="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	395 ljb2_mt="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	396 ljb2_ma="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	397 ljb2_fathmm="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	398 ljb2_gerp="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	399 ljb2_phylop="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	400 ljb2_siphy="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	401
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	402 # parse ljb2 newimpactscores param
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	403 # ljb2_sift, ljb2_pp2hdiv, ljb2_pp2hvar, ljb2_lrt, ljb2_mt, ljb2_ma, ljb2_fathmm, ljb2_gerp++, ljb2_phylop, ljb2_siphy
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	404 if [[ $newimpactscores =~ "ljb2_sift" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	405 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	406 ljb2_sift="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	407 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	408 if [[ $newimpactscores =~ "ljb2_pp2hdiv" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	409 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	410 ljb2_pp2hdiv="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	411 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	412 if [[ $newimpactscores =~ "ljb2_pp2hvar" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	413 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	414 ljb2_pp2hvar="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	415 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	416 if [[ $newimpactscores =~ "ljb2_lrt" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	417 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	418 ljb2_lrt="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	419 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	420 if [[ $newimpactscores =~ "ljb2_mt" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	421 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	422 ljb2_mt="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	423 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	424 if [[ $newimpactscores =~ "ljb2_ma" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	425 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	426 ljb2_ma="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	427 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	428 if [[ $newimpactscores =~ "ljb2_fathmm" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	429 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	430 ljb2_fathmm="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	431 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	432 if [[ $newimpactscores =~ "ljb2_gerp" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	433 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	434 ljb2_gerp="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	435 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	436 if [[ $newimpactscores =~ "ljb2_phylop" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	437 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	438 ljb2_phylop="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	439 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	440 if [[ $newimpactscores =~ "ljb2_siphy" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	441 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	442 ljb2_siphy="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	443 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	444
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	445 if [ $otherinfo == "N" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	446 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	447 otherinfo=""
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	448 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	449
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	450
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	451 #column header names we will be adding
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	452 # ESP 6500
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	453 esp6500si_colheader_ALL="ESP6500si_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	454 esp6500si_colheader_EA="ESP6500si_EA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	455 esp6500si_colheader_AA="ESP6500si_AA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	456 esp6500_colheader_ALL="ESP6500_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	457 esp6500_colheader_EA="ESP6500_EA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	458 esp6500_colheader_AA="ESP6500_AA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	459 esp5400si_colheader_ALL="ESP5400si_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	460 esp5400si_colheader_EA="ESP5400si_EA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	461 esp5400si_colheader_AA="ESP5400si_AA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	462 esp5400_colheader_ALL="ESP5400_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	463 esp5400_colheader_EA="ESP5400_EA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	464 esp5400_colheader_AA="ESP5400_AA"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	465
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	466
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	467 # cg46 cg69
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	468 cg46_colheader="CG_46_genomes"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	469 cg69_colheader="CG_69_genomes"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	470
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	471 cp $infile originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	472 #run annovar or filter only?
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	473 if [ $dorunannovar == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	474 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	475
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	476
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	477 ####################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	478 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	479 # PREPARE INPUT FILE
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	480 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	481 ####################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	482
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	483 echo "converting input file"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	484 vcfheader=""
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	485 if [ $vcf == "Y" ] #if CG varfile, convert
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	486 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	487 # convert vcf to annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	488 $scriptsdir/convert2annovar.pl --format vcf4old --allallele --includeinfo --outfile annovarinput $infile 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	489
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	490 #construct header line from vcf file
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	491 cat $infile \| grep "#CHROM" > additionalcols
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	492 sed -i 's/#//g' additionalcols
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	493 vcfheader="\t`cat additionalcols`"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	494 echo "vcfheader:$vcfheader"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	495 echo -e "chromosome\tbegin\tend\treference\tobserved\t`cat additionalcols`" > originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	496 cat annovarinput >> originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	497
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	498 chrcol=1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	499 startcol=2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	500 endcol=3
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	501 refcol=4
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	502 obscol=5
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	503
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	504
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	505 elif [ $varfile == "Y" ] #if CG varfile, convert
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	506 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	507 # convert varfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	508 $scriptsdir/convert2annovar.pl --format cg --outfile annovarinput $infile 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	509 echo -e "chromosome\tbegin\tend\treference\talleleSeq\tvarType\thaplotype" > originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	510 cat annovarinput \| cut -f1-6,8 >> originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	511 cat annovarinput \| cut -f1-5 >> annovarinput2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	512 mv annovarinput2 annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	513
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	514 chrcol=1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	515 startcol=2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	516 endcol=3
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	517 refcol=4
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	518 obscol=5
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	519
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	520 elif [ $convertcoords == "Y" ] # if CG-coordinates, convert
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	521 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	522 #echo "rearranging columns and converting coordinates"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	523 awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	524 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	525 OFS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	526 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	527 if(FNR>1) {
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	528 gsub(/chr/,"",$"'"${chrcol}"'")
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	529 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	530 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	531 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	532 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	533
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	534 printf("%s\t%s\t%s\t%s\t%s\n" ,$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'");
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	535 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	536 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	537 END{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	538 }' $infile > annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	539
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	540 #remove any "chr" prefixes
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	541 #sed -i '2,$s/chr//g' annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	542
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	543 awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	544 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	545 OFS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	546 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	547
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	548 if(FNR>=1) {
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	549 gsub(/chr/,"",$"'"${chrcol}"'")
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	550 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	551 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	552 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	553 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	554
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	555 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	556 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	557 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	558 END{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	559 }' $infile > originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	560
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	561 #remove any "chr" prefixes
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	562 #sed -i '2,$s/chr//g' originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	563 sed -i 's/omosome/chromosome/g' originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	564
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	565
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	566 else #only rearrange columns if already 1-based coordinates
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	567 echo "rearranging columns "
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	568 awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	569 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	570 OFS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	571 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	572 if(FNR>1) {
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	573 printf("%s\t%s\t%s\t%s\t%s\n",$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'");
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	574 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	575 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	576 END{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	577 }' $infile > annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	578
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	579 #remove any "chr" prefixes
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	580 sed -i '2,$s/chr//g' annovarinput
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	581 sed '2,$s/chr//g' $infile > originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	582 sed -i 's/omosome/chromosome/g' originalfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	583 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	584
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	585 echo "...finished conversion"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	586
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	587
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	588
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	589
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	590 ####################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	591 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	592 # RUN ANNOVAR COMMANDS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	593 #
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	594 ####################################
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	595
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	596
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	597
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	598 ###### gene-based annotation #######
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	599
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	600 # RefSeq Gene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	601 if [ $refgene == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	602 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	603 echo -e "\nrefSeq gene"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	604 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype gene ${hgvs} annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	605
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	606 annovarout=annovarinput.variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	607 sed -i '1i\RefSeq_Func\tRefSeq_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	608 joinresults originalfile $annovarout 3 4 5 6 7 B.RefSeq_Func,B.RefSeq_Gene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	609
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	610 annovarout=annovarinput.exonic_variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	611 sed -i '1i\linenum\tRefSeq_ExonicFunc\tRefSeq_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	612 joinresults originalfile $annovarout 4 5 6 7 8 B.RefSeq_ExonicFunc,B.RefSeq_AAChange
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	613 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	614
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	615
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	616 # UCSC KnownGene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	617 if [ $knowngene == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	618 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	619 echo -e "\nUCSC known gene"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	620 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype knowngene annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	621
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	622 annovarout=annovarinput.variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	623 sed -i '1i\UCSCKnownGene_Func\tUCSCKnownGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	624 joinresults originalfile $annovarout 3 4 5 6 7 B.UCSCKnownGene_Func,B.UCSCKnownGene_Gene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	625
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	626 annovarout=annovarinput.exonic_variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	627 sed -i '1i\linenum\tUCSCKnownGene_ExonicFunc\tUCSCKnownGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	628 joinresults originalfile $annovarout 4 5 6 7 8 B.UCSCKnownGene_ExonicFunc,B.UCSCKnownGene_AAChange
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	629 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	630
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	631
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	632 # Emsembl Gene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	633 if [ $ensgene == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	634 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	635 echo -e "\nEnsembl gene"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	636 $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype ensgene annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	637
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	638 annovarout=annovarinput.variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	639 sed -i '1i\EnsemblGene_Func\tEnsemblGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	640 joinresults originalfile $annovarout 3 4 5 6 7 B.EnsemblGene_Func,B.EnsemblGene_Gene
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	641
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	642 annovarout=annovarinput.exonic_variant_function
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	643 sed -i '1i\linenum\tEnsemblGene_ExonicFunc\tEnsemblGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	644 joinresults originalfile $annovarout 4 5 6 7 8 B.EnsemblGene_ExonicFunc,B.EnsemblGene_AAChange
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	645 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	646
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	647
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	648
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	649 ###### region-based annotation #######
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	650
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	651
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	652 # Transcription Factor Binding Sites Annotation
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	653 if [ $mce == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	654 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	655 echo -e "\nMost Conserved Elements"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	656
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	657 if [ $buildver == "hg18" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	658 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	659 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce44way annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	660 annovarout=annovarinput.${buildver}_phastConsElements44way
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	661 sed -i '1i\db\tphastConsElements44way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	662 joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements44way
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	663
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	664 else #hg19
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	665 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce46way annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	666 annovarout=annovarinput.${buildver}_phastConsElements46way
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	667 sed -i '1i\db\tphastConsElements46way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	668 joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements46way
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	669 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	670
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	671 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	672
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	673
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	674
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	675 # Transcription Factor Binding Sites Annotation
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	676 if [ $tfbs == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	677 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	678 echo -e "\nTranscription Factor Binding Site Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	679 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype tfbs annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	680
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	681 # arguments: originalfile, resultfile,chrcol,startcol,endcol,refcol,obscol,selectcolumns
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	682 annovarout=annovarinput.${buildver}_tfbsConsSites
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	683 sed -i '1i\db\tTFBS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	684 joinresults originalfile $annovarout 3 4 5 6 7 B.TFBS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	685 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	686
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	687
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	688
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	689 # Identify cytogenetic band for genetic variants
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	690 if [ $cytoband == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	691 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	692 echo -e "\nCytogenic band Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	693 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype band annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	694
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	695 annovarout=annovarinput.${buildver}_cytoBand
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	696 sed -i '1i\db\tBand\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	697 joinresults originalfile $annovarout 3 4 5 6 7 B.Band
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	698 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	699
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	700
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	701 # Identify variants located in segmental duplications
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	702 if [ $segdup == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	703 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	704 echo -e "\nSegmental Duplications Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	705 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype segdup annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	706
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	707 annovarout=annovarinput.${buildver}_genomicSuperDups
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	708 sed -i '1i\db\tSegDup\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	709 joinresults originalfile $annovarout 3 4 5 6 7 B.SegDup
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	710 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	711
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	712
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	713
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	714 # Identify previously reported structural variants in DGV
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	715 if [ $dgv == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	716 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	717 echo -e "\nDGV Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	718 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype dgvMerged annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	719
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	720 annovarout=annovarinput.${buildver}_dgvMerged
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	721 sed -i '1i\db\tDGV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	722 joinresults originalfile $annovarout 3 4 5 6 7 B.DGV
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	723 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	724
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	725
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	726 # Identify variants reported in previously published GWAS studies
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	727 if [ $gwas == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	728 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	729 echo -e "\nGWAS Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	730 $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype gwascatalog annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	731
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	732 annovarout=annovarinput.${buildver}_gwasCatalog
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	733 sed -i '1i\db\tGWAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	734 joinresults originalfile $annovarout 3 4 5 6 7 B.GWAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	735 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	736
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	737
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	738
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	739
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	740 ###### filter-based annotation #######
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	741
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	742 #dbSNP
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	743 for version in $dbsnpstr
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	744 do
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	745 if [ $version == "None" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	746 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	747 break
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	748 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	749 echo -e "\ndbSNP region Annotation, version: $version"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	750 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ${version} annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	751
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	752 annovarout=annovarinput.${buildver}_${version}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	753 sed -i '1i\db\tdb'${version}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	754 joinresults originalfile $annovarout 3 4 5 6 7 B.db${version}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	755
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	756
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	757 done
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	758
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	759
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	760
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	761 #1000 Genomes
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	762
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	763 if [ $ver1000g != "None" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	764 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	765
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	766 for version in $g1000str
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	767 do
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	768 #column headers
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	769 g1000_colheader_ALL="${version}_ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	770 g1000_colheader_AFR="${version}_AFR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	771 g1000_colheader_AMR="${version}_AMR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	772 g1000_colheader_ASN="${version}_ASN"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	773 g1000_colheader_EUR="${version}_EUR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	774 g1000_colheader_EAS="${version}_EAS"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	775 g1000_colheader_SAS="${version}_SAS"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	776 g1000_colheader_CEU="${version}_CEU"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	777 g1000_colheader_YRI="${version}_YRI"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	778 g1000_colheader_JPTCHB="${version}_JPTCHB"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	779
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	780 doALL="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	781 doAMR="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	782 doAFR="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	783 doASN="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	784 doEAS="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	785 doSAS="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	786 doEUR="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	787 doCEU="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	788 doYRI="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	789 doJPTCHB="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	790
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	791
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	792 if [ $version == "1000g2012apr" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	793 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	794 fileID="2012_04"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	795 doALL="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	796 if [ $buildver == "hg19" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	797 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	798 doAMR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	799 doAFR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	800 doASN="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	801 doEUR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	802 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	803 elif [ $version == "1000g2014oct" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	804 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	805 fileID="2014_10"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	806 doALL="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	807 doAMR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	808 doAFR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	809 doEUR="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	810 doEAS="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	811 if [ $buildver == "hg19" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	812 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	813 doSAS="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	814 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	815 elif [[ $version == "1000g2012feb" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	816 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	817 fileID="2012_02"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	818 doALL="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	819 elif [[ $version == "1000g2010nov" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	820 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	821 fileID="2010_11"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	822 doALL="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	823 elif [[ $version == "1000g2010jul" && $buildver == "hg18" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	824 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	825 fileID="2010_07"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	826 doALL="N"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	827 doCEU="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	828 doYRI="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	829 doJPTCHB="Y"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	830 else
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	831 echo "unrecognized 1000g version, skipping"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	832 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	833
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	834 #ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	835 if [ $doALL == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	836 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	837 echo -e "\n1000Genomes ALL"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	838 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_all" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	839
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	840 annovarout=annovarinput.${buildver}_ALL.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	841 sed -i '1i\db\t'$g1000_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	842 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	843 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	844
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	845 # AFR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	846 if [ $doAFR == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	847 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	848 echo -e "\n1000Genomes AFR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	849 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_afr" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	850
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	851 annovarout=annovarinput.${buildver}_AFR.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	852 sed -i '1i\db\t'$g1000_colheader_AFR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	853 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AFR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	854 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	855
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	856
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	857 # AMR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	858 if [ $doAMR == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	859 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	860 echo -e "\n1000Genomes AMR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	861 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_amr" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	862
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	863 annovarout=annovarinput.${buildver}_AMR.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	864 sed -i '1i\db\t'$g1000_colheader_AMR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	865 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AMR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	866 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	867
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	868 # ASN
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	869 if [ $doASN == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	870 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	871 echo -e "\n1000Genomes ASN"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	872 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_asn" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	873
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	874 annovarout=annovarinput.${buildver}_ASN.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	875 sed -i '1i\db\t'$g1000_colheader_ASN'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	876 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ASN
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	877 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	878
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	879 # EAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	880 if [ $doEAS == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	881 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	882 echo -e "\n1000Genomes EAS"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	883 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eas" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	884
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	885 annovarout=annovarinput.${buildver}_EAS.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	886 sed -i '1i\db\t'$g1000_colheader_EAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	887 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	888 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	889
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	890 # SAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	891 if [ $doSAS == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	892 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	893 echo -e "\n1000Genomes SAS"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	894 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_sas" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	895
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	896 annovarout=annovarinput.${buildver}_SAS.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	897 sed -i '1i\db\t'$g1000_colheader_SAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	898 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_SAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	899 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	900
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	901 # EUR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	902 if [ $doEUR == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	903 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	904 echo -e "\n1000Genomes EUR"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	905 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eur" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	906
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	907 annovarout=annovarinput.${buildver}_EUR.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	908 sed -i '1i\db\t'$g1000_colheader_EUR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	909 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EUR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	910 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	911
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	912 # CEU
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	913 if [ $doCEU == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	914 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	915 echo -e "\n1000Genomes CEU"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	916 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_ceu" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	917
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	918 annovarout=annovarinput.${buildver}_CEU.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	919 sed -i '1i\db\t'$g1000_colheader_CEU'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	920 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_CEU
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	921 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	922
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	923 # YRI
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	924 if [ $doYRI == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	925 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	926 echo -e "\n1000Genomes YRI"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	927 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_yri" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	928
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	929 annovarout=annovarinput.${buildver}_YRI.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	930 sed -i '1i\db\t'$g1000_colheader_YRI'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	931 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_YRI
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	932
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	933
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	934 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	935
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	936 #JPTCHB
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	937 if [ $doJPTCHB == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	938 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	939 echo -e "\n1000Genomes JPTCHB"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	940 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_jptchb" annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	941
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	942 annovarout=annovarinput.${buildver}_JPTCHB.sites.${fileID}_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	943 sed -i '1i\db\t'$g1000_colheader_JPTCHB'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	944 joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_JPTCHB
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	945 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	946
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	947 done
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	948 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	949
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	950
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	951
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	952
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	953 #### IMPACT SCORE ANNOTATIONS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	954
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	955
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	956 if [ $ljb2_sift == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	957 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	958 echo -e "\nLJB2 SIFT Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	959 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_sift annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	960
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	961 annovarout=annovarinput.${buildver}_ljb2_sift_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	962 sed -i '1i\db\tLJB2_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	963 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SIFT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	964 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	965
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	966 if [ $ljb2_pp2hdiv == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	967 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	968 echo -e "\nLJB2 pp2hdiv Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	969 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hdiv annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	970
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	971 annovarout=annovarinput.${buildver}_ljb2_pp2hdiv_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	972 sed -i '1i\db\tLJB2_PolyPhen2_HDIV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	973 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HDIV
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	974 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	975
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	976 if [ $ljb2_pp2hvar == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	977 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	978 echo -e "\nLJB2 pp2hvar Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	979 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hvar annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	980
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	981 annovarout=annovarinput.${buildver}_ljb2_pp2hvar_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	982
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	983 head $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	984 sed -i '1i\db\tLJB2_PolyPhen2_HVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	985 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HVAR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	986 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	987
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	988 if [ $ljb2_lrt == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	989 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	990 echo -e "\nLJB2 LRT Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	991 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_lrt annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	992
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	993 annovarout=annovarinput.${buildver}_ljb2_lrt_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	994 sed -i '1i\db\tLJB2_LRT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	995 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_LRT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	996 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	997
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	998 if [ $ljb2_mt == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	999 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1000 echo -e "\nLJB2 mutationtaster Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1001 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_mt annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1002
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1003 annovarout=annovarinput.${buildver}_ljb2_mt_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1004 sed -i '1i\db\tLJB2_MutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1005 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationTaster
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1006 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1007
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1008 if [ $ljb2_ma == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1009 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1010 echo -e "\nLJB2 mutationassessor Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1011 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_ma annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1012
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1013 annovarout=annovarinput.${buildver}_ljb2_ma_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1014 sed -i '1i\db\tLJB2_MutationAssessor\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1015 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationAssessor
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1016 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1017
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1018 if [ $ljb2_fathmm == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1019 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1020 echo -e "\nLJB2 FATHMM Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1021 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_fathmm annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1022
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1023 annovarout=annovarinput.${buildver}_ljb2_fathmm_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1024 sed -i '1i\db\tLJB2_FATHMM\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1025 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_FATHMM
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1026 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1027
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1028 if [ $ljb2_gerp == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1029 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1030 echo -e "\nLJB2 GERP++ Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1031 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_gerp++ annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1032
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1033 annovarout=annovarinput.${buildver}_ljb2_gerp++_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1034 sed -i '1i\db\tLJB2_GERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1035 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_GERP++
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1036 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1037
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1038 if [ $ljb2_phylop == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1039 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1040 echo -e "\nLJB2 PhyloP Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1041 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_phylop annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1042
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1043 annovarout=annovarinput.${buildver}_ljb2_phylop_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1044 sed -i '1i\db\tLJB2_PhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1045 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PhyloP
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1046 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1047
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1048 if [ $ljb2_siphy == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1049 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1050 echo -e "\nLJB2 SiPhy Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1051 $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_siphy annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1052
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1053 annovarout=annovarinput.${buildver}_ljb2_siphy_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1054 sed -i '1i\db\tLJB2_SiPhy\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1055 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SiPhy
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1056 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1057
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1058
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1059
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1060 ### OLD IMPACT SCORE ANNOTATIONS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1061
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1062 # SIFT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1063 if [ $avsift == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1064 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1065 echo -e "\nSIFT Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1066 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype avsift annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1067
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1068 annovarout=annovarinput.${buildver}_avsift_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1069 sed -i '1i\db\tAVSIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1070 joinresults originalfile $annovarout 3 4 5 6 7 B.AVSIFT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1071 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1072
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1073 #ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1074 # SIFT2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1075 if [ $ljbsift == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1076 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1077 echo -e "\nLJB SIFT Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1078 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_sift annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1079
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1080 annovarout=annovarinput.${buildver}_ljb_sift_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1081 sed -i '1i\db\tLJB_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1082 joinresults originalfile $annovarout 3 4 5 6 7 B.LJB_SIFT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1083 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1084
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1085
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1086 # PolyPhen2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1087 if [ $polyphen2 == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1088 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1089 echo -e "\nPolyPhen Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1090 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_pp2 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1091
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1092 annovarout=annovarinput.${buildver}_ljb_pp2_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1093 sed -i '1i\db\tPolyPhen2\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1094 joinresults originalfile $annovarout 3 4 5 6 7 B.PolyPhen2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1095 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1096
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1097
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1098 # MutationTaster
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1099 if [ $mutationtaster == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1100 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1101 echo -e "\nMutationTaster Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1102 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_mt annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1103
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1104 annovarout=annovarinput.${buildver}_ljb_mt_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1105 sed -i '1i\db\tMutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1106 joinresults originalfile $annovarout 3 4 5 6 7 B.MutationTaster
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1107 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1108
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1109
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1110 # LRT
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1111 if [ $lrt == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1112 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1113 echo -e "\nLRT Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1114 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_lrt annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1115
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1116 annovarout=annovarinput.${buildver}_ljb_lrt_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1117 sed -i '1i\db\tLikelihoodRatioTestScore\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1118 joinresults originalfile $annovarout 3 4 5 6 7 B.LikelihoodRatioTestScore
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1119 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1120
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1121 # PhyloP
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1122 if [ $phylop == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1123 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1124 echo -e "\nPhyloP Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1125 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_phylop annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1126
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1127 annovarout=annovarinput.${buildver}_ljb_phylop_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1128 sed -i '1i\db\tPhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1129 joinresults originalfile $annovarout 3 4 5 6 7 B.PhyloP
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1130 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1131
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1132
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1133 ### ESP Exome Variant Server
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1134 if [ $esp != "None" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1135 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1136 echo -e "\nESP Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1137 for version in $espstr
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1138 do
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1139 echo "version: $version"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1140 # 6500si ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1141 if [ $version == "esp6500si_all" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1142 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1143 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_all annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1144
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1145 annovarout=annovarinput.${buildver}_esp6500si_all_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1146 sed -i '1i\db\t'$esp6500si_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1147 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1148 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1149
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1150
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1151 # 6500si European American
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1152 if [ $version == "esp6500si_ea" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1153 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1154 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_ea annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1155
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1156 annovarout=annovarinput.${buildver}_esp6500si_ea_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1157 sed -i '1i\db\t'$esp6500si_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1158 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_EA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1159 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1160
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1161 # 6500si African Americans
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1162 if [ $version == "esp6500si_aa" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1163 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1164 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_aa annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1165
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1166 annovarout=annovarinput.${buildver}_esp6500si_aa_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1167 sed -i '1i\db\t'$esp6500si_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1168 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_AA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1169 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1170
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1171
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1172 # 6500 ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1173 if [ $version == "esp6500_all" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1174 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1175 ls
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1176 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_all annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1177
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1178 annovarout=annovarinput.${buildver}_esp6500_all_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1179 sed -i '1i\db\t'$esp6500_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1180 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1181 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1182
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1183
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1184 # 6500 European American
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1185 if [ $version == "esp6500_ea" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1186 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1187 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_ea annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1188 annovarout=annovarinput.${buildver}_esp6500_ea_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1189 sed -i '1i\db\t'$esp6500_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1190 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_EA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1191 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1192
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1193 # 6500 African Americans
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1194 if [ $version == "esp6500_aa" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1195 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1196 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_aa annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1197
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1198 annovarout=annovarinput.${buildver}_esp6500_aa_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1199 sed -i '1i\db\t'$esp6500_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1200 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_AA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1201 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1202
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1203
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1204 # 5400 ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1205 if [ $version == "esp5400_all" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1206 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1207 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_all annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1208
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1209 annovarout=annovarinput.${buildver}_esp5400_all_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1210 sed -i '1i\db\t'$esp5400_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1211 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_ALL
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1212 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1213
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1214
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1215 # 5400 European American
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1216 if [ $version == "esp5400_ea" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1217 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1218 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_ea annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1219
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1220 annovarout=annovarinput.${buildver}_esp5400_ea_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1221 sed -i '1i\db\t'$esp5400_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1222 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_EA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1223 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1224
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1225 # 5400 African Americans
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1226 if [ $version == "esp5400_aa" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1227 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1228 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_aa annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1229
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1230 annovarout=annovarinput.${buildver}_esp5400_aa_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1231 sed -i '1i\db\t'$esp5400_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1232 joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_AA
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1233 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1234
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1235 done
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1236 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1237
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1238
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1239 #exac03
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1240 if [ $exac03 == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1241 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1242 echo -e "\nexac03 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1243 $scriptsdir/annotate_variation.pl --filter -otherinfo --buildver $buildver $otherinfo -dbtype exac03 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1244
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1245 #annovarout.tmp=annovarinput.${buildver}_exac03_dropped
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1246
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1247 # split allelefrequency column into several columns, one per population
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1248 awk 'BEGIN{FS="\t"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1249 OFS="\t"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1250 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1251 gsub(",","\t",$2)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1252 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1253 }END{}' annovarinput.${buildver}_exac03_dropped > $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1254
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1255 head $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1256 sed -i '1i\db\tExAC_Freq\tExAC_AFR\tExAC_AMR\tExAC_EAS\tExAC_FIN\tExAC_NFE\tExAC_OTH\tExAC_SAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1257 joinresults originalfile $annovarout 10 11 12 13 14 B.ExAC_Freq,B.ExAC_AFR,B.ExAC_AMR,B.ExAC_EAS,B.ExAC_FIN,B.ExAC_NFE,B.ExAC_OTH,B.ExAC_SAS
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1258 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1259
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1260 #GERP++
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1261 if [ $gerp == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1262 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1263 echo -e "\nGERP++ Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1264 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype gerp++gt2 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1265
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1266 annovarout="annovarinput.${buildver}_gerp++gt2_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1267 sed -i '1i\db\tGERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1268 joinresults originalfile $annovarout 3 4 5 6 7 B.GERP++
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1269 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1270
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1271
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1272 #COSMIC
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1273 if [[ $cosmic61 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1274 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1275 echo -e "\nCOSMIC61 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1276 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic61 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1277
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1278 annovarout="annovarinput.${buildver}_cosmic61_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1279 sed -i '1i\db\tCOSMIC61\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1280 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC61
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1281
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1282 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1283
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1284 if [[ $cosmic63 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1285 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1286 echo -e "\nCOSMIC63 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1287 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic63 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1288
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1289 annovarout="annovarinput.${buildver}_cosmic63_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1290 sed -i '1i\db\tCOSMIC63\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1291 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC63
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1292
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1293 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1294
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1295 if [[ $cosmic64 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1296 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1297 echo -e "\nCOSMIC64 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1298 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic64 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1299
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1300 annovarout="annovarinput.${buildver}_cosmic64_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1301 sed -i '1i\db\tCOSMIC64\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1302 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC64
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1303
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1304 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1305
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1306 if [[ $cosmic65 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1307 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1308 echo -e "\nCOSMIC65 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1309 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic65 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1310
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1311 annovarout="annovarinput.${buildver}_cosmic65_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1312 sed -i '1i\db\tCOSMIC65\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1313 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC65
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1314
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1315 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1316
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1317 if [[ $cosmic67 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1318 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1319 echo -e "\nCOSMIC67 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1320 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic67 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1321
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1322 annovarout="annovarinput.${buildver}_cosmic67_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1323 sed -i '1i\db\tCOSMIC67\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1324 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC67
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1325
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1326 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1327
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1328 if [[ $cosmic68 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1329 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1330 echo -e "\nCOSMIC68 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1331 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic68 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1332
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1333 annovarout="annovarinput.${buildver}_cosmic68_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1334 sed -i '1i\db\tCOSMIC68\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1335 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC68
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1336
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1337 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1338
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1339 if [[ $cosmic70 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1340 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1341 echo -e "\nCOSMIC70 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1342 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic70 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1343
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1344 annovarout="annovarinput.${buildver}_cosmic70_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1345 sed -i '1i\db\tCOSMIC70\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1346 joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC70
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1347
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1348 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1349
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1350 if [[ $clinvar == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1351 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1352 echo -e "\nCLINVAR Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1353 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20140211 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1354
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1355 annovarout="annovarinput.${buildver}_clinvar_20140211_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1356 sed -i '1i\db\tCLINVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1357 joinresults originalfile $annovarout 3 4 5 6 7 B.CLINVAR
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1358
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1359 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1360
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1361 if [[ $nci60 == "Y" && $buildver == "hg19" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1362 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1363 echo -e "\nNCI60 Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1364 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype nci60 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1365
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1366 annovarout="annovarinput.${buildver}_nci60_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1367 sed -i '1i\db\tNCI60\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1368 joinresults originalfile $annovarout 3 4 5 6 7 B.NCI60
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1369
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1370 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1371
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1372 #cg46
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1373 if [[ $cg46 == "Y" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1374 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1375 echo -e "\nCG 46 genomes Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1376 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg46 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1377
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1378 annovarout="annovarinput.${buildver}_cg46_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1379 sed -i '1i\db\t'${cg46_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1380 joinresults originalfile $annovarout 3 4 5 6 7 B.${cg46_colheader}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1381
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1382 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1383
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1384
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1385 #cg69
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1386 if [[ $cg69 == "Y" ]]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1387 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1388 echo -e "\nCG 69 genomes Annotation"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1389 $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg69 annovarinput $humandb 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1390
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1391 annovarout="annovarinput.${buildver}_cg69_dropped"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1392 sed -i '1i\db\t'${cg69_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1393 joinresults originalfile $annovarout 3 4 5 6 7 B.${cg69_colheader}
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1394
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1395 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1396
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1397
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1398
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1399 if [ $convertcoords == "Y" ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1400 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1401 echo "converting back coordinates"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1402 awk 'BEGIN{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1403 FS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1404 OFS="\t";
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1405 }{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1406 if (FNR==1)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1407 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1408 if(FNR>1) {
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1409 $"'"${chrcol}"'" = "chr"$"'"${chrcol}"'"
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1410 if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" -= 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1411 if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1412 if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" -=1; $"'"${obscol}"'" = "" };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1413 if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" -= 1 };
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1414 print $0
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1415
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1416 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1417 }
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1418 END{
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1419 }' originalfile > originalfile_coords
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1420 else
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1421 mv originalfile originalfile_coords
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1422 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1423
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1424 #restore "chr" prefix?
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1425
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1426 #move to outputfile
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1427 if [ ! -s annovarinput.invalid_input ]
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1428 then
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1429 echo "Congrats, your input file contained no invalid lines!" > annovarinput.invalid_input
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1430 fi
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1431
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1432 cp originalfile_coords $outfile_all
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1433 cp annovarinput.invalid_input $outfile_invalid 2>&1
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1434
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1435 sed -i 's/chrchr/chr/g' $outfile_all
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1436 sed -i 's/chrchr/chr/g' $outfile_invalid
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1437
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1438 fi #if $dorunannovar
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1439
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1440
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1441
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1442
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1443
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1444
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1445
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1446
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1447
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1448
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1449
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1450
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1451
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1452
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1453
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1454
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1455
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1456
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1457
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1458
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1459
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1460
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03 saskia-hiltemann parents: diff changeset	1461

Mercurial > repos > saskia-hiltemann > annovar

annotate tools/tools/annovar/annovar.sh @ 5:4600be69b96f draft