Mercurial > repos > saskia-hiltemann > annovar
changeset 9:f7ff063c738e draft default tip
bugfix for COSMIC70 not giving output
| author | saskia-hiltemann |
|---|---|
| date | Fri, 04 Mar 2016 11:56:10 -0500 |
| parents | d6af2a78617f |
| children | |
| files | tools/annovar/annovar.sh tools/annovar/annovar.xml |
| diffstat | 2 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/tools/annovar/annovar.sh Fri Mar 04 11:32:50 2016 -0500 +++ b/tools/annovar/annovar.sh Fri Mar 04 11:56:10 2016 -0500 @@ -178,7 +178,7 @@ ################################# -set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: exac03nonpsych: exac03nontcga: dbscsnv11: kaviar_20150923: hrcr1: mitimpact2: mitimpact24: dbnsfp30a: spidex: gonl: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage +set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: exac03: exac03nonpsych: exac03nontcga: dbscsnv11: kaviar_20150923: hrcr1: mitimpact2: mitimpact24: dbnsfp30a: spidex: gonl: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: cosmic70: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage [ $# -eq 0 ] && usage @@ -233,6 +233,7 @@ --cosmic65) cosmic65=$2;shift;; # Y or N --cosmic67) cosmic67=$2;shift;; # Y or N --cosmic68) cosmic68=$2;shift;; # Y or N + --cosmic70) cosmic70=$2;shift;; # Y or N --nci60) nci60=$2;shift;; # Y or N --clinvar) clinvar=$2;shift;; # Y or N --filt_dbsnp) filt_dbsnp=$2;shift;; # Y or N
--- a/tools/annovar/annovar.xml Fri Mar 04 11:32:50 2016 -0500 +++ b/tools/annovar/annovar.xml Fri Mar 04 11:56:10 2016 -0500 @@ -20,6 +20,7 @@ --cosmic65 "${cosmic65}" --cosmic67 "${cosmic67}" --cosmic68 "${cosmic68}" + --cosmic70 "${cosmic70}" --outall "${annotated}" --outinvalid "${invalid}" --dorunannovar "${dorun}"