# HG changeset patch
# User saskia-hiltemann
# Date 1384788753 18000
# Node ID 565c0e69023814fbe770a8d19711e3d4681aa234
# Parent 7d9353127f8a4af161919b3650e4cf76fd6496d7
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
Fixed dgv annotation to use new UCSC table dgvMerged instead.
diff -r 7d9353127f8a -r 565c0e690238 README
--- a/README Tue Nov 05 07:16:32 2013 -0500
+++ b/README Mon Nov 18 10:32:33 2013 -0500
@@ -33,181 +33,210 @@
list of files in my own humandb folder:
- hg18_ALL.sites.2012_04.txt
- hg18_ALL.sites.2012_04.txt.idx
- hg18_avsift.txt
- hg18_avsift.txt.idx
- hg18_CEU.sites.2010_07.txt
- hg18_CEU.sites.2010_07.txt.idx
- hg18_cg46.txt
- hg18_cg46.txt.idx
- hg18_cg69.txt
- hg18_cg69.txt.idx
- hg18_cytoBand.txt
- hg18_dgv.txt
- hg18_ensGeneMrna.fa
- hg18_ensGene.txt
- hg18_esp5400_aa.txt
- hg18_esp5400_aa.txt.idx
- hg18_esp5400_all.txt
- hg18_esp5400_all.txt.idx
- hg18_esp5400_ea.txt
- hg18_esp5400_ea.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_JPTCHB.sites.2010_07.txt
- hg18_JPTCHB.sites.2010_07.txt.idx
- hg18_keggMapDesc.txt
- hg18_keggPathway.txt
- hg18_kgXref.txt
- hg18_knownGeneMrna.fa
- hg18_knownGene.txt
- 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
- hg18_ljb_sift.txt
- hg18_ljb_sift.txt.idx
- hg18_phastConsElements44way.txt
- hg18_refGeneMrna.fa
- hg18_refGene.txt
- hg18_refLink.txt
- hg18_snp128NonFlagged.txt
- hg18_snp128NonFlagged.txt.idx
- hg18_snp128.txt
- hg18_snp128.txt.idx
- hg18_snp129NonFlagged.txt
- hg18_snp129NonFlagged.txt.idx
- hg18_snp129.txt
- hg18_snp129.txt.idx
- hg18_snp130NonFlagged.txt
- hg18_snp130NonFlagged.txt.idx
- hg18_snp130.txt
- hg18_snp130.txt.idx
- hg18_snp131NonFlagged.txt
- hg18_snp131NonFlagged.txt.idx
- hg18_snp131.txt
- hg18_snp131.txt.idx
- hg18_snp132NonFlagged.txt
- hg18_snp132NonFlagged.txt.idx
- hg18_snp132.txt
- hg18_snp132.txt.idx
- hg18_tfbsConsSites.txt
- hg18_YRI.sites.2010_07.txt
- hg18_YRI.sites.2010_07.txt.idx
- 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_avsift.txt
- hg19_avsift.txt.idx
- hg19_cg46.txt
- hg19_cg46.txt.idx
- hg19_cg69.txt
- hg19_cg69.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_cytoBand.txt
- hg19_dgv.txt
- hg19_ensGeneMrna.fa
- hg19_ensGene.txt
- hg19_esp5400_aa.txt
- hg19_esp5400_aa.txt.idx
- hg19_esp5400_all.txt
- hg19_esp5400_all.txt.idx
- hg19_esp5400_ea.txt
- hg19_esp5400_ea.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_EUR.sites.2012_04.txt
- hg19_EUR.sites.2012_04.txt.idx
- hg19_genomicSuperDups.txt
- hg19_gerp++gt2.txt
- hg19_gerp++gt2.txt.idx
- hg19_gwasCatalog.txt
- hg19_keggMapDesc.txt
- hg19_keggPathway.txt
- hg19_kgXref.txt
- hg19_knownGeneMrna.fa
- hg19_knownGene.txt
- 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
- hg19_ljb_sift.txt
- hg19_ljb_sift.txt.idx
- hg19_phastConsElements46way.txt
- hg19_refGeneMrna.fa
- hg19_refGene.txt
- hg19_refLink.txt
- hg19_snp130NonFlagged.txt
- hg19_snp130NonFlagged.txt.idx
- hg19_snp130.txt
- hg19_snp130.txt.idx
- hg19_snp131NonFlagged.txt
- hg19_snp131NonFlagged.txt.idx
- hg19_snp131.txt
- hg19_snp132NonFlagged.txt
- hg19_snp132NonFlagged.txt.idx
- hg19_snp132.txt
- hg19_snp132.txt.idx
- hg19_snp135NonFlagged.txt
- hg19_snp135NonFlagged.txt.idx
- hg19_snp135.txt
- hg19_snp137NonFlagged.txt
- hg19_snp137NonFlagged.txt.idx
- hg19_snp137.txt
- hg19_tfbsConsSites.txt
+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 7d9353127f8a -r 565c0e690238 README~
--- a/README~ Tue Nov 05 07:16:32 2013 -0500
+++ b/README~ Mon Nov 18 10:32:33 2013 -0500
@@ -141,6 +141,8 @@
hg19_cosmic63.txt.idx
hg19_cosmic64.txt
hg19_cosmic64.txt.idx
+ hg19_cosmic65.txt
+ hg19_cosmic65.txt.idx
hg19_cytoBand.txt
hg19_dgv.txt
hg19_ensGeneMrna.fa
diff -r 7d9353127f8a -r 565c0e690238 tool-data/annovar.loc.sample
--- a/tool-data/annovar.loc.sample Tue Nov 05 07:16:32 2013 -0500
+++ b/tool-data/annovar.loc.sample Mon Nov 18 10:32:33 2013 -0500
@@ -2,5 +2,5 @@
#
# value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb
-hg18 hg18 build 36 (hg18) /path/to/annovarscripts /path/to/humandb
-hg19 hg19 build 37 (hg19) /path/to/annovarscripts /path/to/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 7d9353127f8a -r 565c0e690238 tools/annovar/annovar.sh
--- a/tools/annovar/annovar.sh Tue Nov 05 07:16:32 2013 -0500
+++ b/tools/annovar/annovar.sh Mon Nov 18 10:32:33 2013 -0500
@@ -1,7 +1,12 @@
#!/bin/bash
test="N"
+dofilter="N"
+#########################
+# DEFINE SOME
+# FUNCTIONS
+#########################
function usage(){
echo "usage: $0 todo"
@@ -167,7 +172,14 @@
-set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: esp: gerp: cosmic61: cosmic63: cosmic64: cosmic65: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage
+#################################
+#
+# PARSE PARAMETERS
+#
+#################################
+
+
+set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage
[ $# -eq 0 ] && usage
@@ -176,8 +188,8 @@
do
case "$1" in
--inputfile) infile=$2;shift;; # inputfile
- --buildver) buildver=$2;shift;; # hg18 or hg19
- --humandb) humandb=$2;shift;; # location of humandb database
+ --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
@@ -188,6 +200,7 @@
--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")"
--tfbs) tfbs=$2;shift;; # Y or N
--mce) mce=$2;shift;; # Y or N
@@ -199,13 +212,18 @@
--cg46) cg46=$2;shift;;
--cg69) cg69=$2;shift;;
--impactscores) impactscores=$2;shift;; # Y or N
- --scriptsdir) scriptsdir=$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
--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
+ --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
@@ -220,8 +238,7 @@
--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
- --dofilter) dofilter=$2;shift;; #Y or N
+ --dorunannovar) dorunannovar=$2;shift;; #Y or N
-h) shift;;
--) shift;break;;
-*) usage;;
@@ -230,6 +247,11 @@
shift
done
+#sometimes galaxy screws up these variables after updates, if comma-separated list, use only what is before first comma
+humandb=${humandbtmp%,*}
+buildver=${buildvertmp%,*}
+scriptsdir=${scriptsdirtmp%,*}
+
if [ $test == "Y" ]
then
@@ -249,6 +271,7 @@
echo "cg46: ${cg46}"
echo "cg69: ${cg69}"
echo "impactscores: $impactscores"
+ echo "impactscores: $newimpactscores"
echo "esp: $esp"
echo "gerp: $gerp"
echo "cosmic: $cosmic"
@@ -277,10 +300,18 @@
fi
+
+############################################
+#
+# Annotate Variants
+#
+############################################
+
+#parse geneanno param
refgene="N"
knowngene="N"
ensgene="N"
-#parse geneanno param
+
if [[ $geneanno =~ "refSeq" ]]
then
refgene="Y"
@@ -293,7 +324,10 @@
then
ensgene="Y"
fi
-
+if [ $hgvs == "N" ]
+then
+ hgvs=""
+fi
#parse verdbsnp/1000g/esp strings
dbsnpstr=${verdbsnp//,/ }
@@ -314,7 +348,8 @@
polyphen2="N"
phylop="N"
ljbsift="N"
-#parse impactscores param
+
+#parse old impactscores param (obsolete)
if [[ $impactscores =~ "mutationtaster" ]]
then
mutationtaster="Y"
@@ -331,6 +366,10 @@
then
ljbsift="Y"
fi
+if [[ $impactscores =~ "ljb2sift" ]]
+then
+ ljb2sift="Y"
+fi
if [[ $impactscores =~ "pp2" ]]
then
polyphen2="Y"
@@ -347,6 +386,65 @@
#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
@@ -498,7 +596,7 @@
if [ $refgene == "Y" ]
then
echo -e "\nrefSeq gene"
- $scriptsdir/annotate_variation.pl --geneanno --buildver $buildver -dbtype gene annovarinput $humandb 2>&1
+ $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
@@ -612,9 +710,9 @@
if [ $dgv == "Y" ]
then
echo -e "\nDGV Annotation"
- $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype dgv annovarinput $humandb 2>&1
+ $scriptsdir/annotate_variation.pl --regionanno --buildver $buildver -dbtype dgvMerged annovarinput $humandb 2>&1
- annovarout=annovarinput.${buildver}_dgv
+ 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
@@ -807,6 +905,115 @@
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
+ 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
@@ -822,7 +1029,7 @@
# SIFT2
if [ $ljbsift == "Y" ]
then
- echo -e "\nSIFT Annotation"
+ 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
@@ -984,35 +1191,6 @@
fi
- #ESP6500
- if [ $esp == "Y" ]
- then
- echo -e "\nESP Annotation OLD"
- # ALL
- $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'$esp6500_colheader_ALL'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
- joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_ALL
-
-
- # European American
- $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'$esp6500_colheader_EA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
- joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_EA
-
- # African Americans
- $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'$esp6500_colheader_AA'\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout
- joinresults originalfile $annovarout 3 4 5 6 7 B.$esp6500_colheader_AA
- fi
-
-
-
#GERP++
if [ $gerp == "Y" ]
then
@@ -1070,6 +1248,39 @@
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 [[ $clinvar == "Y" && $buildver == "hg19" ]]
+ then
+ echo -e "\nCLINVAR Annotation"
+ $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20131105 annovarinput $humandb 2>&1
+
+ annovarout="annovarinput.${buildver}_clinvar_20131105_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
@@ -1138,52 +1349,6 @@
-############################################
-#
-# Filter Annotated Variants
-#
-############################################
-
-
-if [[ $dofilter == "Y" ]]
-then
- echo "starting filtering"
- cp originalfile filteredfile
-
- ### do the filtering
- # usage: runfilter (-1=do not filter, 0=filter any value)
-
- #1000genomes
- runfilter filteredfile ${g1000_colheader_ALL} ${threshold_1000g_ALL}
- runfilter filteredfile ${g1000_colheader_AFR} ${threshold_1000g_AFR}
- runfilter filteredfile ${g1000_colheader_AMR} ${threshold_1000g_AMR}
- runfilter filteredfile ${g1000_colheader_ASN} ${threshold_1000g_ASN}
- runfilter filteredfile ${g1000_colheader_EUR} ${threshold_1000g_EUR}
-
- #esp
- runfilter filteredfile ${esp6500_colheader_ALL} ${threshold_ESP6500_ALL}
- runfilter filteredfile ${esp6500_colheader_EA} ${threshold_ESP6500_EA}
- runfilter filteredfile ${esp6500_colheader_AA} ${threshold_ESP6500_AA}
-
- #dbsnp
- for version in $filt_dbsnpstr
- do
- if [ $version == "None" ]
- then
- break
- fi
- runfilter filteredfile "db$version" "text" #-42 will filter any non-empty string in that field
-
- done
-
- #complete genomics
- runfilter filteredfile ${cg46_colheader} ${threshold_cg46}
- runfilter filteredfile ${cg69_colheader} ${threshold_cg69}
-
- #move filtered output file to galaxy output file
- cp filteredfile $outfile_filt
-
-fi
@@ -1201,3 +1366,4 @@
+
diff -r 7d9353127f8a -r 565c0e690238 tools/annovar/annovar.xml
--- a/tools/annovar/annovar.xml Tue Nov 05 07:16:32 2013 -0500
+++ b/tools/annovar/annovar.xml Mon Nov 18 10:32:33 2013 -0500
@@ -7,13 +7,13 @@
annovar.sh
- --impactscores ${impactscores}
--esp ${esp}
--gerp ${gerp}
--cosmic61 ${cosmic61}
--cosmic63 ${cosmic63}
--cosmic64 ${cosmic64}
- --cosmic65 ${cosmic65}
+ --cosmic65 ${cosmic65}
+ --cosmic67 ${cosmic67}
--outall ${annotated}
--outinvalid ${invalid}
--dorunannovar ${dorun}
@@ -57,6 +57,10 @@
--cg46 ${cgfortysix}
--cg69 ${cgsixtynine}
--ver1000g ${ver1000g}
+ --hgvs ${hgvs}
+ --otherinfo ${otherinfo}
+ --newimpactscores ${newimpactscores}
+ --clinvar ${clinvar}
@@ -98,7 +102,8 @@
-
+
+
@@ -154,14 +159,32 @@
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -196,13 +219,23 @@
Input Formats may be one of the following:
- VCF file
-
- Complete Genomics varfile
+VCF file
+Complete Genomics varfile
+
+Custom tab-delimited file (specify chromosome, start, end, reference allele, observed allele columns)
- 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**
- Custom tab-delimited CG-derived file (specify chromosome, start, end, reference allele, observed allele, varType columns)
+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.