# HG changeset patch # User saskia-hiltemann # Date 1445958070 14400 # Node ID 69e2067a120dca80c962d3c3617aa61e0d8daf2e # Parent a3b16fd125c35e7731a9ec44242f8b9e7dd8e1c5 Uploaded diff -r a3b16fd125c3 -r 69e2067a120d tools/README --- a/tools/README Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,242 +0,0 @@ -ANNOVAR needs to be installed manually in the following way: - - -1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of - the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) -1b) Restart galaxy instance for changes in .loc file to take effect - - -2) If you do not have ANNOVAR installed, request annovar download and sign license here: - http://www.openbioinformatics.org/annovar/annovar_download_form.php - - 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts. - tool uses annotate_variation.pl and convert2annovar.pl - - 4) Then download all desired databases for all desired builds as follows: - annotate_variation.pl -downdb -buildver [-webfrom annovar] - - where is location where all database files should be stored - and is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool) - and can be hg18 or hg19 for humans, also other organisms available. - - list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html - - 5) edit the tool-data/annovar.loc file to reflect location of humandb folder - 5b) restart galaxy instance for changes in .loc file to take effect - -6) Tool uses cgatools join for combining of files, this should be installed automatically with repository. If not, get a copy from Complete Genomics directly: - wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz - tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz - - and place the "cgatools" binary found in bin/ directory on your $PATH - - -list of files in my own humandb folder: - -hg18_ALL.sites.2012_04.txt -hg18_ALL.sites.2012_04.txt.idx -hg18_CEU.sites.2010_07.txt -hg18_CEU.sites.2010_07.txt.idx -hg18_JPTCHB.sites.2010_07.txt -hg18_JPTCHB.sites.2010_07.txt.idx -hg18_YRI.sites.2010_07.txt -hg18_YRI.sites.2010_07.txt.idx -hg18_cg46.txt -hg18_cg46.txt.idx -hg18_cg69.txt -hg18_cg69.txt.idx -hg18_cytoBand.txt -hg18_dgvMerged.txt -hg18_ensGene.txt -hg18_ensGeneMrna.fa -hg18_esp5400_aa.txt -hg18_esp5400_aa.txt.idx -hg18_esp5400_all.txt -hg18_esp5400_all.txt.idx -hg18_esp6500_aa.txt -hg18_esp6500_aa.txt.idx -hg18_esp6500_all.txt -hg18_esp6500_all.txt.idx -hg18_esp6500_ea.txt -hg18_esp6500_ea.txt.idx -hg18_esp6500si_aa.txt -hg18_esp6500si_aa.txt.idx -hg18_esp6500si_all.txt -hg18_esp6500si_all.txt.idx -hg18_esp6500si_ea.txt -hg18_esp6500si_ea.txt.idx -hg18_example_db_generic.txt -hg18_example_db_gff3.txt -hg18_genomicSuperDups.txt -hg18_gerp++gt2.txt -hg18_gerp++gt2.txt.idx -hg18_gwasCatalog.txt -hg18_kgXref.txt -hg18_knownGene.txt -hg18_knownGeneMrna.fa -hg18_ljb2_fathmm.txt -hg18_ljb2_fathmm.txt.idx -hg18_ljb2_gerp++.txt -hg18_ljb2_gerp++.txt.idx -hg18_ljb2_ma.txt -hg18_ljb2_ma.txt.idx -hg18_ljb2_mt.txt -hg18_ljb2_mt.txt.idx -hg18_ljb2_phylop.txt -hg18_ljb2_phylop.txt.idx -hg18_ljb2_pp2hdiv.txt -hg18_ljb2_pp2hdiv.txt.idx -hg18_ljb2_pp2hvar.txt -hg18_ljb2_pp2hvar.txt.idx -hg18_ljb2_sift.txt -hg18_ljb2_sift.txt.idx -hg18_ljb2_siphy.txt -hg18_ljb2_siphy.txt.idx -hg18_phastConsElements44way.txt -hg18_refGene.txt -hg18_refGeneMrna.fa -hg18_refLink.txt -hg18_snp128.txt -hg18_snp128.txt.idx -hg18_snp128NonFlagged.txt -hg18_snp128NonFlagged.txt.idx -hg18_snp129.txt -hg18_snp129.txt.idx -hg18_snp129NonFlagged.txt -hg18_snp129NonFlagged.txt.idx -hg18_snp130.txt -hg18_snp130.txt.idx -hg18_snp130NonFlagged.txt -hg18_snp130NonFlagged.txt.idx -hg18_snp131.txt -hg18_snp131.txt.idx -hg18_snp131NonFlagged.txt -hg18_snp131NonFlagged.txt.idx -hg18_snp132.txt -hg18_snp132.txt.idx -hg18_snp132NonFlagged.txt -hg18_snp132NonFlagged.txt.idx -hg18_tfbsConsSites.txt -hg19_AFR.sites.2012_04.txt -hg19_AFR.sites.2012_04.txt.idx -hg19_ALL.sites.2010_11.txt -hg19_ALL.sites.2010_11.txt.idx -hg19_ALL.sites.2012_02.txt -hg19_ALL.sites.2012_02.txt.idx -hg19_ALL.sites.2012_04.txt -hg19_ALL.sites.2012_04.txt.idx -hg19_AMR.sites.2012_04.txt -hg19_AMR.sites.2012_04.txt.idx -hg19_ASN.sites.2012_04.txt -hg19_ASN.sites.2012_04.txt.idx -hg19_EUR.sites.2012_04.txt -hg19_EUR.sites.2012_04.txt.idx -hg19_avsift.txt -hg19_avsift.txt.idx -hg19_cg46.txt -hg19_cg46.txt.idx -hg19_cg69.txt -hg19_cg69.txt.idx -hg19_clinvar_20131105.txt -hg19_clinvar_20131105.txt.idx -hg19_cosmic61.txt -hg19_cosmic61.txt.idx -hg19_cosmic63.txt -hg19_cosmic63.txt.idx -hg19_cosmic64.txt -hg19_cosmic64.txt.idx -hg19_cosmic65.txt -hg19_cosmic65.txt.idx -hg19_cosmic67.txt -hg19_cytoBand.txt -hg19_dgvMerged.txt -hg19_ensGene.txt -hg19_ensGeneMrna.fa -hg19_esp5400_aa.txt -hg19_esp5400_aa.txt.idx -hg19_esp5400_all.txt -hg19_esp5400_all.txt.idx -hg19_esp6500_aa.txt -hg19_esp6500_aa.txt.idx -hg19_esp6500_all.txt -hg19_esp6500_all.txt.idx -hg19_esp6500_ea.txt -hg19_esp6500_ea.txt.idx -hg19_esp6500si_aa.txt -hg19_esp6500si_aa.txt.idx -hg19_esp6500si_all.txt -hg19_esp6500si_all.txt.idx -hg19_esp6500si_ea.txt -hg19_esp6500si_ea.txt.idx -hg19_genomicSuperDups.txt -hg19_gerp++gt2.txt -hg19_gerp++gt2.txt.idx -hg19_gwasCatalog.txt -hg19_kgXref.txt -hg19_knownGene.txt -hg19_knownGeneMrna.fa -hg19_ljb2_fathmm.txt -hg19_ljb2_fathmm.txt.idx -hg19_ljb2_gerp++.txt -hg19_ljb2_gerp++.txt.idx -hg19_ljb2_ma.txt -hg19_ljb2_ma.txt.idx -hg19_ljb2_mt.txt -hg19_ljb2_phylop.txt -hg19_ljb2_phylop.txt.idx -hg19_ljb2_pp2hdiv.txt -hg19_ljb2_pp2hdiv.txt.idx -hg19_ljb2_pp2hvar.txt -hg19_ljb2_pp2hvar.txt.idx -hg19_ljb2_sift.txt -hg19_ljb2_sift.txt.idx -hg19_ljb2_siphy.txt -hg19_nci60.txt -hg19_nci60.txt.idx -hg19_phastConsElements46way.txt -hg19_refGene.txt -hg19_refGeneMrna.fa -hg19_refLink.txt -hg19_snp130.txt -hg19_snp130.txt.idx -hg19_snp130NonFlagged.txt -hg19_snp130NonFlagged.txt.idx -hg19_snp131.txt -hg19_snp131NonFlagged.txt -hg19_snp131NonFlagged.txt.idx -hg19_snp132.txt -hg19_snp132.txt.idx -hg19_snp132NonFlagged.txt -hg19_snp132NonFlagged.txt.idx -hg19_snp135.txt -hg19_snp135NonFlagged.txt -hg19_snp135NonFlagged.txt.idx -hg19_snp137.txt -hg19_snp137NonFlagged.txt -hg19_snp137NonFlagged.txt.idx -hg19_tfbsConsSites.txt - - -obsolete functional impact database files: (disabled by default) -hg18_avsift.txt -hg18_avsift.txt.idx -hg19_ljb_all.txt -hg19_ljb_all.txt.idx -hg19_ljb_lrt.txt -hg19_ljb_lrt.txt.idx -hg19_ljb_mt.txt -hg19_ljb_mt.txt.idx -hg19_ljb_phylop.txt -hg19_ljb_phylop.txt.idx -hg19_ljb_pp2.txt -hg19_ljb_pp2.txt.idx -hg18_ljb_all.txt -hg18_ljb_all.txt.idx -hg18_ljb_lrt.txt -hg18_ljb_lrt.txt.idx -hg18_ljb_mt.txt -hg18_ljb_mt.txt.idx -hg18_ljb_phylop.txt -hg18_ljb_phylop.txt.idx -hg18_ljb_pp2.txt -hg18_ljb_pp2.txt.idx diff -r a3b16fd125c3 -r 69e2067a120d tools/annovar/annovar.sh --- a/tools/annovar/annovar.sh Thu Oct 01 04:47:19 2015 -0400 +++ b/tools/annovar/annovar.sh Tue Oct 27 11:01:10 2015 -0400 @@ -821,7 +821,7 @@ doSAS="Y" fi - elif [[ $version == "1000g2015aug" && $buildver == "hg19" ]] + elif [[ $version == "1000g2015aug" ]] then fileID="2015_08" doALL="Y" @@ -831,15 +831,15 @@ doEAS="Y" doSAS="Y" - elif [[ $version == "1000g2012feb" && $buildver == "hg19" ]] + elif [[ $version == "1000g2012feb" ]] then fileID="2012_02" doALL="Y" - elif [[ $version == "1000g2010nov" && $buildver == "hg19" ]] + elif [[ $version == "1000g2010nov" ]] then fileID="2010_11" doALL="Y" - elif [[ $version == "1000g2010jul" && $buildver == "hg18" ]] + elif [[ $version == "1000g2010jul" ]] then fileID="2010_07" doALL="N" @@ -1279,7 +1279,7 @@ if [ $gonl == "Y" ] then - if [ $buildver == "hg19" ] + if [ $buildver == "hg19" ] then echo -e "\nGoNL Annotation" $scriptsdir/annotate_variation.pl --filter --buildver $buildver --otherinfo -dbtype generic -genericdbfile ${buildver}_gonl.txt annovarinput $humandb 2>&1 diff -r a3b16fd125c3 -r 69e2067a120d tools/annovar/annovar.xml --- a/tools/annovar/annovar.xml Thu Oct 01 04:47:19 2015 -0400 +++ b/tools/annovar/annovar.xml Tue Oct 27 11:01:10 2015 -0400 @@ -1,4 +1,4 @@ - + Annotate a file using ANNOVAR @@ -75,7 +75,7 @@ - + @@ -113,7 +113,7 @@ - + @@ -139,12 +139,12 @@ - + - - + + @@ -167,7 +167,7 @@ - + @@ -176,16 +176,19 @@ - - - + + + + + + - + diff -r a3b16fd125c3 -r 69e2067a120d tools/tool-data/annovar.loc.sample --- a/tools/tool-data/annovar.loc.sample Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#loc file for annovar tool -# -# value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb - -#hg18 hg18 hg18 [Human Mar. 2006 (NCBI36/hg18)] /path/to/annovarscripts /path/to/humandb -#hg19 hg19 hg19 [Human Feb. 2009 (GRCh37/hg19)] /path/to/annovarscripts /path/to/humandb diff -r a3b16fd125c3 -r 69e2067a120d tools/tool_data_table_conf.xml.sample --- a/tools/tool_data_table_conf.xml.sample Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ - - - -value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb - -
-
diff -r a3b16fd125c3 -r 69e2067a120d tools/tool_dependencies.xml --- a/tools/tool_dependencies.xml Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - - - - - http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz - chmod a+x bin/cgatools - - bin/cgatools - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - $REPOSITORY_INSTALL_DIR - - - - - Downloads and installs the cgatools binary. - - - - diff -r a3b16fd125c3 -r 69e2067a120d tools/tools/annovar/annovar.sh --- a/tools/tools/annovar/annovar.sh Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1461 +0,0 @@ -#!/bin/bash - -test="N" -dofilter="N" - -######################### -# DEFINE SOME -# FUNCTIONS -######################### - -function usage(){ - echo "usage: $0 todo" -} - -function runfilter(){ - ifile=$1 - columnname=$2 - threshold=$3 - - if [[ $threshold == "-1" ]] - then - echo "not filtering" - return - fi - - echo "filtering: $columnname, $threshold" - cat $ifile - - #get column number corresponding to column header - column=`awk 'BEGIN{ - FS="\t"; - col=-1 - }{ - if(FNR==1){ - for(i=1;i<=NF;i++){ - if($i == "'"${columnname}"'") - col=i - } - print col - } - }' $ifile ` - - if [ $column == -1 ] - then - echo "no such column, exiting" - return - fi - - #perform filtering using the threshold - awk 'BEGIN{ - FS="\t"; - OFS="\t"; - }{ - if(FNR==1) - print $0; - if(FNR>1){ - if( $"'"${column}"'" == "" ) # empty column, then print - print $0 - else if ("'"${threshold}"'" == "text"){} #if set to text dont check threshold - - else if ($"'"${column}"'" < "'"${threshold}"'") #else do check it - print $0 - } - }' $ifile > tmpfile - - mv tmpfile $ifile -} - -# arguments: originalfile,resultfile,chrcol,startcol,endcol,refcol,obscol,addcols -function joinresults(){ - ofile=$1 - rfile=$2 - colchr=$3 - colstart=$4 - colend=$5 - colref=$6 - colobs=$7 - addcols=$8 #e.g. "B.col1,B.col2" - - test="N" - - # echo "joining result with original file" - if [ $test == "Y" ] - then - echo "ofile: $ofile" - head $ofile - echo "rfile: $rfile" - head $rfile - fi - numlines=`wc $rfile | cut -d" " -f2` - - # if empty results file, just add header fields - if [[ ! -s $rfile ]] - then - dummycol=${addcols:2} - outputcol=${dummycol//",B."/" "} - numcommas=`echo "$addcols" | grep -o "," | wc -l` - - awk 'BEGIN{FS="\t";OFS="\t"}{ - if(FNR==1) - print $0,"'"$outputcol"'"; - else{ - printf $0 - for(i=0;i<="'"$numcommas"'"+1;i++) - printf "\t" - printf "\n" - } - }END{}' $ofile > tempofile - - mv tempofile $ofile - return - fi - - - #get input file column names for cgatools join - col_chr_name=`head -1 $rfile | cut -f${colchr}` - col_start_name=`head -1 $rfile | cut -f${colstart}` - col_end_name=`head -1 $rfile | cut -f${colend}` - col_ref_name=`head -1 $rfile | cut -f${colref}` - col_obs_name=`head -1 $rfile | cut -f${colobs}` - - #get annotation file column names for cgatools join - chr_name=`head -1 $ofile | cut -f${chrcol}` - start_name=`head -1 $ofile | cut -f${startcol}` - end_name=`head -1 $ofile | cut -f${endcol}` - ref_name=`head -1 $ofile | cut -f${refcol}` - obs_name=`head -1 $ofile | cut -f${obscol}` - - if [ $test == "Y" ] - then - echo "input file" - echo "chr col: $col_chr_name ($colchr)" - echo "start col: $col_start_name ($colstart)" - echo "end col: $col_end_name ($colend)" - echo "ref col: $col_ref_name ($colref)" - echo "obs col: $col_obs_name ($colobs)" - echo "" - echo "annotation file" - echo "chr col: $chr_name ($chrcol)" - echo "start col: $start_name ($startcol)" - echo "end col: $end_name ($endcol)" - echo "ref col: $ref_name ($refcol)" - echo "obs col: $obs_name ($obscol)" - fi - - #perform join - cgatools join --beta \ - --input $ofile $rfile \ - --output temporiginal \ - --match ${chr_name}:${col_chr_name} \ - --match ${start_name}:${col_start_name} \ - --match ${end_name}:${col_end_name} \ - --match ${ref_name}:${col_ref_name} \ - --match ${obs_name}:${col_obs_name} \ - --select A.*,$addcols \ - --always-dump \ - --output-mode compact - - #replace originalfile - sed -i 's/^>//g' temporiginal #join sometimes adds a '>' symbol to header - mv temporiginal originalfile - - if [ $test == "Y" ] - then - echo "joining complete" - head originalfile - echo "" - fi - -} - - - - -################################# -# -# PARSE PARAMETERS -# -################################# - - -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 -[ $# -eq 0 ] && usage - - - -while [ $# -gt 0 ] -do - case "$1" in - --inputfile) infile=$2;shift;; # inputfile - --buildver) buildvertmp=$2;shift;; # hg18 or hg19 - --humandb) humandbtmp=$2;shift;; # location of humandb database - --varfile) varfile=$2;shift;; # Y or N - --VCF) vcf=$2;shift;; #Y or N - --chrcol) chrcol=$2;shift;; # which column has chr - --startcol) startcol=$2;shift;; # which column has start - --endcol) endcol=$2;shift;; # which column has end - --refcol) refcol=$2;shift;; # which column has ref - --obscol) obscol=$2;shift;; # which column has alt - --vartypecol) vartypecol=$2;shift;; # which column has vartype - --convertcoords) convertcoords=$2;shift;; # Y or N convert coordinate from CG to 1-based? - --geneanno) geneanno=$2;shift;; # comma-separated list of strings refSeq, knowngene, ensgene - --hgvs) hgvs=$2;shift;; - --verdbsnp) verdbsnp=$2;shift;; #comma-separated list of dbsnp version to annotate with (e.g. "132,135NonFlagged,137,138")" - --tfbs) tfbs=$2;shift;; # Y or N - --mce) mce=$2;shift;; # Y or N - --cytoband) cytoband=$2;shift;; # Y or N - --segdup) segdup=$2;shift;; # Y or N - --dgv) dgv=$2;shift;; # Y or N - --gwas) gwas=$2;shift;; # Y or N - --ver1000g) ver1000g=$2;shift;; # Y or N - --cg46) cg46=$2;shift;; - --cg69) cg69=$2;shift;; - --impactscores) impactscores=$2;shift;; # Y or N - --newimpactscores) newimpactscores=$2;shift;; # Y or N - --otherinfo) otherinfo=$2;shift;; - --scriptsdir) scriptsdirtmp=$2;shift;; # Y or N - --esp) esp=$2;shift;; # Y or N - --exac03) exac03=$2;shift;; - --gerp) gerp=$2;shift;; # Y or N - --cosmic61) cosmic61=$2;shift;; # Y or N - --cosmic63) cosmic63=$2;shift;; # Y or N - --cosmic64) cosmic64=$2;shift;; # Y or N - --cosmic65) cosmic65=$2;shift;; # Y or N - --cosmic67) cosmic67=$2;shift;; # Y or N - --cosmic68) cosmic68=$2;shift;; # Y or N - --nci60) nci60=$2;shift;; # Y or N - --clinvar) clinvar=$2;shift;; # Y or N - --filt_dbsnp) filt_dbsnp=$2;shift;; - --filt1000GALL) threshold_1000g_ALL=$2;shift;; #threshold value - --filt1000GAFR) threshold_1000g_AFR=$2;shift;; #threshold value - --filt1000GAMR) threshold_1000g_AMR=$2;shift;; #threshold value - --filt1000GASN) threshold_1000g_ASN=$2;shift;; #threshold value - --filt1000GEUR) threshold_1000g_EUR=$2;shift;; #threshold value - --filtESP6500ALL) threshold_ESP6500_ALL=$2;shift;; #threshold value - --filtESP6500EA) threshold_ESP6500_EA=$2;shift;; #threshold value - --filtESP6500AA) threshold_ESP6500_AA=$2;shift;; #threshold value - --filtcg46) threshold_cg46=$2;shift;; - --filtcg69) threshold_cg69=$2;shift;; - --outall) outfile_all=$2;shift;; # file - --outfilt) outfile_filt=$2;shift;; # file - --outinvalid) outfile_invalid=$2;shift;; #file - --dorunannovar) dorunannovar=$2;shift;; #Y or N - -h) shift;; - --) shift;break;; - -*) usage;; - *) break;; - esac - shift -done - -#sometimes galaxy screws up these variables after updates, if comma-separated list, use only what is before first comma -humandb=${humandbtmp%,*} -buildver=${buildvertmp%,*} -scriptsdir=${scriptsdirtmp%,*} - - -if [ $test == "Y" ] -then - echo "dorunannovar: $dorunannovar" - echo "infile: $infile" - echo "buildver: $buildver" - echo "annovardb: $humandb" - echo "verdbnsp: $verdbsnp" - echo "geneanno: $geneanno" - echo "tfbs: $tfbs" - echo "mce: $mce" - echo "cytoband: $cytoband" - echo "segdup: $segdup" - echo "dgv: $dgv" - echo "gwas: $gwas" - echo "g1000: ${g1000}" - echo "cg46: ${cg46}" - echo "cg69: ${cg69}" - echo "impactscores: $impactscores" - echo "impactscores: $newimpactscores" - echo "esp: $esp" - echo "gerp: $gerp" - echo "cosmic: $cosmic" - echo "outfile: $outfile_all" - echo "outinvalid: $outfile_invalid" - echo "outfiltered: $outfile_filt" - echo "varfile: $varfile" - echo "vcf" $vcf - echo "chrcol: $chrcol" - echo "startcol: $startcol" - echo "endcol: $endcol" - echo "refcol: $refcol" - echo "obscol: $obscol" - echo "convertcoords: $convertcoords" - echo "vartypecol: $vartypecol" - echo "dofilter: $dofilter" - echo "threshold_1000g_ALL : $threshold_1000g_ALL" - echo "threshold_1000g_AFR : $threshold_1000g_AFR" - echo "threshold_1000g_AMR : $threshold_1000g_AMR" - echo "threshold_1000g_ASN : $threshold_1000g_ASN" - echo "threshold_1000g_EUR : $threshold_1000g_EUR" - echo "threshold_ESP6500_ALL: $threshold_ESP6500_ALL" - echo "threshold_ESP6500_EA : $threshold_ESP6500_EA" - echo "threshold_ESP6500_AA : $threshold_ESP6500_AA" - -fi - - - -############################################ -# -# Annotate Variants -# -############################################ - -#parse geneanno param -refgene="N" -knowngene="N" -ensgene="N" - -if [[ $geneanno =~ "refSeq" ]] -then - refgene="Y" -fi -if [[ $geneanno =~ "knowngene" ]] -then - knowngene="Y" -fi -if [[ $geneanno =~ "ensgene" ]] -then - ensgene="Y" -fi -if [ $hgvs == "N" ] -then - hgvs="" -fi - -#parse verdbsnp/1000g/esp strings -dbsnpstr=${verdbsnp//,/ } -filt_dbsnpstr=${filt_dbsnp//,/ } -g1000str=${ver1000g//,/ } -espstr=${esp//,/ } - -if [ $test == "Y" ] -then - echo "annotate dbsnp: $dbsnpstr" - echo "annotate esp: $espstr" - echo "filter dbsnp: $filt_dbsnpstr" -fi - -mutationtaster="N" -avsift="N" -lrt="N" -polyphen2="N" -phylop="N" -ljbsift="N" - -#parse old impactscores param (obsolete) -if [[ $impactscores =~ "mutationtaster" ]] -then - mutationtaster="Y" -fi -if [[ $impactscores =~ "sift" ]] -then - avsift="Y" -fi -if [[ $impactscores =~ "lrt" ]] -then - lrt="Y" -fi -if [[ $impactscores =~ "ljbsift" ]] -then - ljbsift="Y" -fi -if [[ $impactscores =~ "ljb2sift" ]] -then - ljb2sift="Y" -fi -if [[ $impactscores =~ "pp2" ]] -then - polyphen2="Y" -fi -if [[ $impactscores =~ "phylop" ]] -then - phylop="Y" -fi - -if [[ $varfile == "Y" ]] -then - convertcoords="Y" -fi - -#ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores - -ljb2_sift="N" -ljb2_pp2hdiv="N" -ljb2_pp2hvar="N" -ljb2_lrt="N" -ljb2_mt="N" -ljb2_ma="N" -ljb2_fathmm="N" -ljb2_gerp="N" -ljb2_phylop="N" -ljb2_siphy="N" - -# parse ljb2 newimpactscores param -# ljb2_sift, ljb2_pp2hdiv, ljb2_pp2hvar, ljb2_lrt, ljb2_mt, ljb2_ma, ljb2_fathmm, ljb2_gerp++, ljb2_phylop, ljb2_siphy -if [[ $newimpactscores =~ "ljb2_sift" ]] -then - ljb2_sift="Y" -fi -if [[ $newimpactscores =~ "ljb2_pp2hdiv" ]] -then - ljb2_pp2hdiv="Y" -fi -if [[ $newimpactscores =~ "ljb2_pp2hvar" ]] -then - ljb2_pp2hvar="Y" -fi -if [[ $newimpactscores =~ "ljb2_lrt" ]] -then - ljb2_lrt="Y" -fi -if [[ $newimpactscores =~ "ljb2_mt" ]] -then - ljb2_mt="Y" -fi -if [[ $newimpactscores =~ "ljb2_ma" ]] -then - ljb2_ma="Y" -fi -if [[ $newimpactscores =~ "ljb2_fathmm" ]] -then - ljb2_fathmm="Y" -fi -if [[ $newimpactscores =~ "ljb2_gerp" ]] -then - ljb2_gerp="Y" -fi -if [[ $newimpactscores =~ "ljb2_phylop" ]] -then - ljb2_phylop="Y" -fi -if [[ $newimpactscores =~ "ljb2_siphy" ]] -then - ljb2_siphy="Y" -fi - -if [ $otherinfo == "N" ] -then - otherinfo="" -fi - - -#column header names we will be adding -# ESP 6500 -esp6500si_colheader_ALL="ESP6500si_ALL" -esp6500si_colheader_EA="ESP6500si_EA" -esp6500si_colheader_AA="ESP6500si_AA" -esp6500_colheader_ALL="ESP6500_ALL" -esp6500_colheader_EA="ESP6500_EA" -esp6500_colheader_AA="ESP6500_AA" -esp5400si_colheader_ALL="ESP5400si_ALL" -esp5400si_colheader_EA="ESP5400si_EA" -esp5400si_colheader_AA="ESP5400si_AA" -esp5400_colheader_ALL="ESP5400_ALL" -esp5400_colheader_EA="ESP5400_EA" -esp5400_colheader_AA="ESP5400_AA" - - -# cg46 cg69 -cg46_colheader="CG_46_genomes" -cg69_colheader="CG_69_genomes" - -cp $infile originalfile -#run annovar or filter only? -if [ $dorunannovar == "Y" ] -then - - - #################################### - # - # PREPARE INPUT FILE - # - #################################### - - echo "converting input file" - vcfheader="" - if [ $vcf == "Y" ] #if CG varfile, convert - then - # convert vcf to annovarinput - $scriptsdir/convert2annovar.pl --format vcf4old --allallele --includeinfo --outfile annovarinput $infile 2>&1 - - #construct header line from vcf file - cat $infile | grep "#CHROM" > additionalcols - sed -i 's/#//g' additionalcols - vcfheader="\t`cat additionalcols`" - echo "vcfheader:$vcfheader" - echo -e "chromosome\tbegin\tend\treference\tobserved\t`cat additionalcols`" > originalfile - cat annovarinput >> originalfile - - chrcol=1 - startcol=2 - endcol=3 - refcol=4 - obscol=5 - - - elif [ $varfile == "Y" ] #if CG varfile, convert - then - # convert varfile - $scriptsdir/convert2annovar.pl --format cg --outfile annovarinput $infile 2>&1 - echo -e "chromosome\tbegin\tend\treference\talleleSeq\tvarType\thaplotype" > originalfile - cat annovarinput | cut -f1-6,8 >> originalfile - cat annovarinput | cut -f1-5 >> annovarinput2 - mv annovarinput2 annovarinput - - chrcol=1 - startcol=2 - endcol=3 - refcol=4 - obscol=5 - - elif [ $convertcoords == "Y" ] # if CG-coordinates, convert - then - #echo "rearranging columns and converting coordinates" - awk 'BEGIN{ - FS="\t"; - OFS="\t"; - }{ - if(FNR>1) { - gsub(/chr/,"",$"'"${chrcol}"'") - if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 }; - if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" }; - if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" }; - if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 }; - - printf("%s\t%s\t%s\t%s\t%s\n" ,$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'"); - } - } - END{ - }' $infile > annovarinput - - #remove any "chr" prefixes - #sed -i '2,$s/chr//g' annovarinput - - awk 'BEGIN{ - FS="\t"; - OFS="\t"; - }{ - - if(FNR>=1) { - gsub(/chr/,"",$"'"${chrcol}"'") - if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" += 1 }; - if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "-" }; - if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" +=1; $"'"${obscol}"'" = "-" }; - if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" += 1 }; - - print $0 - } - } - END{ - }' $infile > originalfile - - #remove any "chr" prefixes - #sed -i '2,$s/chr//g' originalfile - sed -i 's/omosome/chromosome/g' originalfile - - - else #only rearrange columns if already 1-based coordinates - echo "rearranging columns " - awk 'BEGIN{ - FS="\t"; - OFS="\t"; - }{ - if(FNR>1) { - printf("%s\t%s\t%s\t%s\t%s\n",$"'"${chrcol}"'",$"'"${startcol}"'",$"'"${endcol}"'",$"'"${refcol}"'",$"'"${obscol}"'"); - } - } - END{ - }' $infile > annovarinput - - #remove any "chr" prefixes - sed -i '2,$s/chr//g' annovarinput - sed '2,$s/chr//g' $infile > originalfile - sed -i 's/omosome/chromosome/g' originalfile - fi - - echo "...finished conversion" - - - - - #################################### - # - # RUN ANNOVAR COMMANDS - # - #################################### - - - - ###### gene-based annotation ####### - - # RefSeq Gene - if [ $refgene == "Y" ] - then - echo -e "\nrefSeq gene" - $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype gene ${hgvs} annovarinput $humandb 2>&1 - - annovarout=annovarinput.variant_function - sed -i '1i\RefSeq_Func\tRefSeq_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.RefSeq_Func,B.RefSeq_Gene - - annovarout=annovarinput.exonic_variant_function - sed -i '1i\linenum\tRefSeq_ExonicFunc\tRefSeq_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 4 5 6 7 8 B.RefSeq_ExonicFunc,B.RefSeq_AAChange - fi - - - # UCSC KnownGene - if [ $knowngene == "Y" ] - then - echo -e "\nUCSC known gene" - $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype knowngene annovarinput $humandb 2>&1 - - annovarout=annovarinput.variant_function - sed -i '1i\UCSCKnownGene_Func\tUCSCKnownGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.UCSCKnownGene_Func,B.UCSCKnownGene_Gene - - annovarout=annovarinput.exonic_variant_function - sed -i '1i\linenum\tUCSCKnownGene_ExonicFunc\tUCSCKnownGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 4 5 6 7 8 B.UCSCKnownGene_ExonicFunc,B.UCSCKnownGene_AAChange - fi - - - # Emsembl Gene - if [ $ensgene == "Y" ] - then - echo -e "\nEnsembl gene" - $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype ensgene annovarinput $humandb 2>&1 - - annovarout=annovarinput.variant_function - sed -i '1i\EnsemblGene_Func\tEnsemblGene_Gene\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.EnsemblGene_Func,B.EnsemblGene_Gene - - annovarout=annovarinput.exonic_variant_function - sed -i '1i\linenum\tEnsemblGene_ExonicFunc\tEnsemblGene_AAChange\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 4 5 6 7 8 B.EnsemblGene_ExonicFunc,B.EnsemblGene_AAChange - fi - - - - ###### region-based annotation ####### - - - # Transcription Factor Binding Sites Annotation - if [ $mce == "Y" ] - then - echo -e "\nMost Conserved Elements" - - if [ $buildver == "hg18" ] - then - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce44way annovarinput $humandb 2>&1 - annovarout=annovarinput.${buildver}_phastConsElements44way - sed -i '1i\db\tphastConsElements44way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements44way - - else #hg19 - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype mce46way annovarinput $humandb 2>&1 - annovarout=annovarinput.${buildver}_phastConsElements46way - sed -i '1i\db\tphastConsElements46way\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.phastConsElements46way - fi - - fi - - - - # Transcription Factor Binding Sites Annotation - if [ $tfbs == "Y" ] - then - echo -e "\nTranscription Factor Binding Site Annotation" - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype tfbs annovarinput $humandb 2>&1 - - # arguments: originalfile, resultfile,chrcol,startcol,endcol,refcol,obscol,selectcolumns - annovarout=annovarinput.${buildver}_tfbsConsSites - sed -i '1i\db\tTFBS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.TFBS - fi - - - - # Identify cytogenetic band for genetic variants - if [ $cytoband == "Y" ] - then - echo -e "\nCytogenic band Annotation" - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype band annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_cytoBand - sed -i '1i\db\tBand\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.Band - fi - - - # Identify variants located in segmental duplications - if [ $segdup == "Y" ] - then - echo -e "\nSegmental Duplications Annotation" - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype segdup annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_genomicSuperDups - sed -i '1i\db\tSegDup\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.SegDup - fi - - - - # Identify previously reported structural variants in DGV - if [ $dgv == "Y" ] - then - echo -e "\nDGV Annotation" - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype dgvMerged annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_dgvMerged - sed -i '1i\db\tDGV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.DGV - fi - - - # Identify variants reported in previously published GWAS studies - if [ $gwas == "Y" ] - then - echo -e "\nGWAS Annotation" - $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype gwascatalog annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_gwasCatalog - sed -i '1i\db\tGWAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.GWAS - fi - - - - - ###### filter-based annotation ####### - - #dbSNP - for version in $dbsnpstr - do - if [ $version == "None" ] - then - break - fi - echo -e "\ndbSNP region Annotation, version: $version" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ${version} annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_${version}_dropped - sed -i '1i\db\tdb'${version}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.db${version} - - - done - - - - #1000 Genomes - - if [ $ver1000g != "None" ] - then - - for version in $g1000str - do - #column headers - g1000_colheader_ALL="${version}_ALL" - g1000_colheader_AFR="${version}_AFR" - g1000_colheader_AMR="${version}_AMR" - g1000_colheader_ASN="${version}_ASN" - g1000_colheader_EUR="${version}_EUR" - g1000_colheader_EAS="${version}_EAS" - g1000_colheader_SAS="${version}_SAS" - g1000_colheader_CEU="${version}_CEU" - g1000_colheader_YRI="${version}_YRI" - g1000_colheader_JPTCHB="${version}_JPTCHB" - - doALL="N" - doAMR="N" - doAFR="N" - doASN="N" - doEAS="N" - doSAS="N" - doEUR="N" - doCEU="N" - doYRI="N" - doJPTCHB="N" - - - if [ $version == "1000g2012apr" ] - then - fileID="2012_04" - doALL="Y" - if [ $buildver == "hg19" ] - then - doAMR="Y" - doAFR="Y" - doASN="Y" - doEUR="Y" - fi - elif [ $version == "1000g2014oct" ] - then - fileID="2014_10" - doALL="Y" - doAMR="Y" - doAFR="Y" - doEUR="Y" - doEAS="Y" - if [ $buildver == "hg19" ] - then - doSAS="Y" - fi - elif [[ $version == "1000g2012feb" && $buildver == "hg19" ]] - then - fileID="2012_02" - doALL="Y" - elif [[ $version == "1000g2010nov" && $buildver == "hg19" ]] - then - fileID="2010_11" - doALL="Y" - elif [[ $version == "1000g2010jul" && $buildver == "hg18" ]] - then - fileID="2010_07" - doALL="N" - doCEU="Y" - doYRI="Y" - doJPTCHB="Y" - else - echo "unrecognized 1000g version, skipping" - fi - - #ALL - if [ $doALL == "Y" ] - then - echo -e "\n1000Genomes ALL" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_all" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ALL.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ALL - fi - - # AFR - if [ $doAFR == "Y" ] - then - echo -e "\n1000Genomes AFR" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_afr" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_AFR.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_AFR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AFR - fi - - - # AMR - if [ $doAMR == "Y" ] - then - echo -e "\n1000Genomes AMR" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_amr" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_AMR.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_AMR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_AMR - fi - - # ASN - if [ $doASN == "Y" ] - then - echo -e "\n1000Genomes ASN" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_asn" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ASN.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_ASN'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_ASN - fi - - # EAS - if [ $doEAS == "Y" ] - then - echo -e "\n1000Genomes EAS" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eas" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_EAS.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_EAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EAS - fi - - # SAS - if [ $doSAS == "Y" ] - then - echo -e "\n1000Genomes SAS" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_sas" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_SAS.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_SAS'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_SAS - fi - - # EUR - if [ $doEUR == "Y" ] - then - echo -e "\n1000Genomes EUR" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_eur" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_EUR.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_EUR'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_EUR - fi - - # CEU - if [ $doCEU == "Y" ] - then - echo -e "\n1000Genomes CEU" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_ceu" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_CEU.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_CEU'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_CEU - fi - - # YRI - if [ $doYRI == "Y" ] - then - echo -e "\n1000Genomes YRI" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_yri" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_YRI.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_YRI'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_YRI - - - fi - - #JPTCHB - if [ $doJPTCHB == "Y" ] - then - echo -e "\n1000Genomes JPTCHB" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype "${version}_jptchb" annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_JPTCHB.sites.${fileID}_dropped - sed -i '1i\db\t'$g1000_colheader_JPTCHB'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$g1000_colheader_JPTCHB - fi - - done - fi - - - - - #### IMPACT SCORE ANNOTATIONS - - - if [ $ljb2_sift == "Y" ] - then - echo -e "\nLJB2 SIFT Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_sift annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_sift_dropped - sed -i '1i\db\tLJB2_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SIFT - fi - - if [ $ljb2_pp2hdiv == "Y" ] - then - echo -e "\nLJB2 pp2hdiv Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hdiv annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_pp2hdiv_dropped - sed -i '1i\db\tLJB2_PolyPhen2_HDIV\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HDIV - fi - - if [ $ljb2_pp2hvar == "Y" ] - then - echo -e "\nLJB2 pp2hvar Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_pp2hvar annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_pp2hvar_dropped - - head $annovarout - sed -i '1i\db\tLJB2_PolyPhen2_HVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PolyPhen2_HVAR - fi - - if [ $ljb2_lrt == "Y" ] - then - echo -e "\nLJB2 LRT Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_lrt annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_lrt_dropped - sed -i '1i\db\tLJB2_LRT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_LRT - fi - - if [ $ljb2_mt == "Y" ] - then - echo -e "\nLJB2 mutationtaster Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_mt annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_mt_dropped - sed -i '1i\db\tLJB2_MutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationTaster - fi - - if [ $ljb2_ma == "Y" ] - then - echo -e "\nLJB2 mutationassessor Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_ma annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_ma_dropped - sed -i '1i\db\tLJB2_MutationAssessor\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_MutationAssessor - fi - - if [ $ljb2_fathmm == "Y" ] - then - echo -e "\nLJB2 FATHMM Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_fathmm annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_fathmm_dropped - sed -i '1i\db\tLJB2_FATHMM\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_FATHMM - fi - - if [ $ljb2_gerp == "Y" ] - then - echo -e "\nLJB2 GERP++ Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_gerp++ annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_gerp++_dropped - sed -i '1i\db\tLJB2_GERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_GERP++ - fi - - if [ $ljb2_phylop == "Y" ] - then - echo -e "\nLJB2 PhyloP Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_phylop annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_phylop_dropped - sed -i '1i\db\tLJB2_PhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_PhyloP - fi - - if [ $ljb2_siphy == "Y" ] - then - echo -e "\nLJB2 SiPhy Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver $otherinfo -dbtype ljb2_siphy annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb2_siphy_dropped - sed -i '1i\db\tLJB2_SiPhy\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB2_SiPhy - fi - - - - ### OLD IMPACT SCORE ANNOTATIONS - - # SIFT - if [ $avsift == "Y" ] - then - echo -e "\nSIFT Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype avsift annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_avsift_dropped - sed -i '1i\db\tAVSIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.AVSIFT - fi - - #ljb refers to Liu, Jian, Boerwinkle paper in Human Mutation with pubmed ID 21520341. Cite this paper if you use the scores - # SIFT2 - if [ $ljbsift == "Y" ] - then - echo -e "\nLJB SIFT Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_sift annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb_sift_dropped - sed -i '1i\db\tLJB_SIFT\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LJB_SIFT - fi - - - # PolyPhen2 - if [ $polyphen2 == "Y" ] - then - echo -e "\nPolyPhen Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_pp2 annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb_pp2_dropped - sed -i '1i\db\tPolyPhen2\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.PolyPhen2 - fi - - - # MutationTaster - if [ $mutationtaster == "Y" ] - then - echo -e "\nMutationTaster Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_mt annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb_mt_dropped - sed -i '1i\db\tMutationTaster\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.MutationTaster - fi - - - # LRT - if [ $lrt == "Y" ] - then - echo -e "\nLRT Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_lrt annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb_lrt_dropped - sed -i '1i\db\tLikelihoodRatioTestScore\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.LikelihoodRatioTestScore - fi - - # PhyloP - if [ $phylop == "Y" ] - then - echo -e "\nPhyloP Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype ljb_phylop annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_ljb_phylop_dropped - sed -i '1i\db\tPhyloP\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.PhyloP - fi - - - ### ESP Exome Variant Server - if [ $esp != "None" ] - then - echo -e "\nESP Annotation" - for version in $espstr - do - echo "version: $version" - # 6500si ALL - if [ $version == "esp6500si_all" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_all annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp6500si_all_dropped - sed -i '1i\db\t'$esp6500si_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_ALL - fi - - - # 6500si European American - if [ $version == "esp6500si_ea" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_ea annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp6500si_ea_dropped - sed -i '1i\db\t'$esp6500si_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_EA - fi - - # 6500si African Americans - if [ $version == "esp6500si_aa" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500si_aa annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp6500si_aa_dropped - sed -i '1i\db\t'$esp6500si_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500si_colheader_AA - fi - - - # 6500 ALL - if [ $version == "esp6500_all" ] - then - ls - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_all annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp6500_all_dropped - sed -i '1i\db\t'$esp6500_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'" ' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_ALL - fi - - - # 6500 European American - if [ $version == "esp6500_ea" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_ea annovarinput $humandb 2>&1 - annovarout=annovarinput.${buildver}_esp6500_ea_dropped - sed -i '1i\db\t'$esp6500_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_EA - fi - - # 6500 African Americans - if [ $version == "esp6500_aa" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp6500_aa annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp6500_aa_dropped - sed -i '1i\db\t'$esp6500_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_AA - fi - - - # 5400 ALL - if [ $version == "esp5400_all" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_all annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp5400_all_dropped - sed -i '1i\db\t'$esp5400_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_ALL - fi - - - # 5400 European American - if [ $version == "esp5400_ea" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_ea annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp5400_ea_dropped - sed -i '1i\db\t'$esp5400_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_EA - fi - - # 5400 African Americans - if [ $version == "esp5400_aa" ] - then - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype esp5400_aa annovarinput $humandb 2>&1 - - annovarout=annovarinput.${buildver}_esp5400_aa_dropped - sed -i '1i\db\t'$esp5400_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.$esp5400_colheader_AA - fi - - done - fi - - - #exac03 - if [ $exac03 == "Y" ] - then - echo -e "\nexac03 Annotation" - $scriptsdir/annotate_variation.pl --filter -otherinfo --buildver $buildver $otherinfo -dbtype exac03 annovarinput $humandb 2>&1 - - #annovarout.tmp=annovarinput.${buildver}_exac03_dropped - - # split allelefrequency column into several columns, one per population - awk 'BEGIN{FS="\t" - OFS="\t" - }{ - gsub(",","\t",$2) - print $0 - }END{}' annovarinput.${buildver}_exac03_dropped > $annovarout - - head $annovarout - sed -i '1i\db\tExAC_Freq\tExAC_AFR\tExAC_AMR\tExAC_EAS\tExAC_FIN\tExAC_NFE\tExAC_OTH\tExAC_SAS\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - 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 - fi - - #GERP++ - if [ $gerp == "Y" ] - then - echo -e "\nGERP++ Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype gerp++gt2 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_gerp++gt2_dropped" - sed -i '1i\db\tGERP++\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.GERP++ - fi - - - #COSMIC - if [[ $cosmic61 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC61 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic61 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic61_dropped" - sed -i '1i\db\tCOSMIC61\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC61 - - fi - - if [[ $cosmic63 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC63 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic63 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic63_dropped" - sed -i '1i\db\tCOSMIC63\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC63 - - fi - - if [[ $cosmic64 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC64 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic64 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic64_dropped" - sed -i '1i\db\tCOSMIC64\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC64 - - fi - - if [[ $cosmic65 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC65 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic65 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic65_dropped" - sed -i '1i\db\tCOSMIC65\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC65 - - fi - - if [[ $cosmic67 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC67 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic67 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic67_dropped" - sed -i '1i\db\tCOSMIC67\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC67 - - fi - - if [[ $cosmic68 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC68 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic68 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic68_dropped" - sed -i '1i\db\tCOSMIC68\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC68 - - fi - - if [[ $cosmic70 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCOSMIC70 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic70 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cosmic70_dropped" - sed -i '1i\db\tCOSMIC70\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC70 - - fi - - if [[ $clinvar == "Y" && $buildver == "hg19" ]] - then - echo -e "\nCLINVAR Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20140211 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_clinvar_20140211_dropped" - sed -i '1i\db\tCLINVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.CLINVAR - - fi - - if [[ $nci60 == "Y" && $buildver == "hg19" ]] - then - echo -e "\nNCI60 Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype nci60 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_nci60_dropped" - sed -i '1i\db\tNCI60\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.NCI60 - - fi - - #cg46 - if [[ $cg46 == "Y" ]] - then - echo -e "\nCG 46 genomes Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg46 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cg46_dropped" - sed -i '1i\db\t'${cg46_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.${cg46_colheader} - - fi - - - #cg69 - if [[ $cg69 == "Y" ]] - then - echo -e "\nCG 69 genomes Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cg69 annovarinput $humandb 2>&1 - - annovarout="annovarinput.${buildver}_cg69_dropped" - sed -i '1i\db\t'${cg69_colheader}'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout - joinresults originalfile $annovarout 3 4 5 6 7 B.${cg69_colheader} - - fi - - - - if [ $convertcoords == "Y" ] - then - echo "converting back coordinates" - awk 'BEGIN{ - FS="\t"; - OFS="\t"; - }{ - if (FNR==1) - print $0 - if(FNR>1) { - $"'"${chrcol}"'" = "chr"$"'"${chrcol}"'" - if( $"'"${vartypecol}"'" == "snp" ){ $"'"${startcol}"'" -= 1 }; - if( $"'"${vartypecol}"'" == "ins" ){ $"'"${refcol}"'" = "" }; - if( $"'"${vartypecol}"'" == "del" ){ $"'"${startcol}"'" -=1; $"'"${obscol}"'" = "" }; - if( $"'"${vartypecol}"'" == "sub" ){ $"'"${startcol}"'" -= 1 }; - print $0 - - } - } - END{ - }' originalfile > originalfile_coords - else - mv originalfile originalfile_coords - fi - - #restore "chr" prefix? - - #move to outputfile - if [ ! -s annovarinput.invalid_input ] - then - echo "Congrats, your input file contained no invalid lines!" > annovarinput.invalid_input - fi - - cp originalfile_coords $outfile_all - cp annovarinput.invalid_input $outfile_invalid 2>&1 - - sed -i 's/chrchr/chr/g' $outfile_all - sed -i 's/chrchr/chr/g' $outfile_invalid - -fi #if $dorunannovar - - - - - - - - - - - - - - - - - - - - - - - diff -r a3b16fd125c3 -r 69e2067a120d tools/tools/annovar/annovar.xml --- a/tools/tools/annovar/annovar.xml Thu Oct 01 04:47:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,255 +0,0 @@ - - Annotate a file using ANNOVAR - - - cgatools - - - - annovar.sh - --esp ${esp} - --exac03 ${exac03} - --gerp ${gerp} - --cosmic61 ${cosmic61} - --cosmic63 ${cosmic63} - --cosmic64 ${cosmic64} - --cosmic65 ${cosmic65} - --cosmic67 ${cosmic67} - --cosmic68 ${cosmic68} - --outall ${annotated} - --outinvalid ${invalid} - --dorunannovar ${dorun} - --inputfile ${infile} - --buildver ${reference.fields.dbkey} - --humandb ${reference.fields.ANNOVAR_humandb} - --scriptsdir ${reference.fields.ANNOVAR_scripts} - --verdbsnp ${verdbsnp} - --geneanno ${geneanno} - --tfbs ${tfbs} - --mce ${mce} - --cytoband ${cytoband} - --segdup ${segdup} - --dgv ${dgv} - --gwas ${gwas} - #if $filetype.type == "other" - --varfile N - --VCF N - --chrcol ${filetype.col_chr} - --startcol ${filetype.col_start} - --endcol ${filetype.col_end} - --obscol ${filetype.col_obs} - --refcol ${filetype.col_ref} - - #if $filetype.convertcoords.convert == "Y" - --vartypecol ${filetype.convertcoords.col_vartype} - --convertcoords Y - #else - --convertcoords N - #end if - #end if - #if $filetype.type == "vcf" - --varfile N - --VCF Y - --convertcoords N - #end if - #if $filetype.type == "varfile" - --varfile Y - --VCF N - #end if - --cg46 ${cgfortysix} - --cg69 ${cgsixtynine} - --ver1000g ${ver1000g} - --hgvs ${hgvs} - --otherinfo ${otherinfo} - --newimpactscores ${newimpactscores} - --clinvar ${clinvar} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -This tool will annotate a file using ANNOVAR. - -**ANNOVAR Website and Documentation** - -Website: http://www.openbioinformatics.org/annovar/ - -Paper: http://nar.oxfordjournals.org/content/38/16/e164 - -**Input Formats** - -Input Formats may be one of the following: - -VCF file -Complete Genomics varfile - -Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns) - -Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns) - - -**Database Notes** - -see ANNOVAR website for extensive documentation, a few notes on some of the databases: - -**LJB2 Database** - -PolyPhen2 HVAR should be used for diagnostics of Mendelian diseases, which requires distinguishing mutations with drastic effects from all the remaining human variation, including abundant mildly deleterious alleles.The authors recommend calling probably damaging if the score is between 0.909 and 1, and possibly damaging if the score is between 0.447 and 0.908, and benign if the score is between 0 and 0.446. - -PolyPhen HDIV should be used when evaluating rare alleles at loci potentially involved in complex phenotypes, dense mapping of regions identified by genome-wide association studies, and analysis of natural selection from sequence data. The authors recommend calling probably damaging if the score is between 0.957 and 1, and possibly damaging if the score is between 0.453 and 0.956, and benign is the score is between 0 and 0.452. - - - - - -