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comparison tools/annovar/annovar.sh @ 9:f7ff063c738e draft default tip

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bugfix for COSMIC70 not giving output
author saskia-hiltemann
date Fri, 04 Mar 2016 11:56:10 -0500
parents d6af2a78617f
children
comparison
equal deleted inserted replaced
8:d6af2a78617f 9:f7ff063c738e
176 # PARSE PARAMETERS 176 # PARSE PARAMETERS
177 # 177 #
178 ################################# 178 #################################
179 179
180 180
181 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 181 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
182 [ $# -eq 0 ] && usage 182 [ $# -eq 0 ] && usage
183 183
184 184
185 185
186 while [ $# -gt 0 ] 186 while [ $# -gt 0 ]
231 --cosmic63) cosmic63=$2;shift;; # Y or N 231 --cosmic63) cosmic63=$2;shift;; # Y or N
232 --cosmic64) cosmic64=$2;shift;; # Y or N 232 --cosmic64) cosmic64=$2;shift;; # Y or N
233 --cosmic65) cosmic65=$2;shift;; # Y or N 233 --cosmic65) cosmic65=$2;shift;; # Y or N
234 --cosmic67) cosmic67=$2;shift;; # Y or N 234 --cosmic67) cosmic67=$2;shift;; # Y or N
235 --cosmic68) cosmic68=$2;shift;; # Y or N 235 --cosmic68) cosmic68=$2;shift;; # Y or N
236 --cosmic70) cosmic70=$2;shift;; # Y or N
236 --nci60) nci60=$2;shift;; # Y or N 237 --nci60) nci60=$2;shift;; # Y or N
237 --clinvar) clinvar=$2;shift;; # Y or N 238 --clinvar) clinvar=$2;shift;; # Y or N
238 --filt_dbsnp) filt_dbsnp=$2;shift;; # Y or N 239 --filt_dbsnp) filt_dbsnp=$2;shift;; # Y or N
239 --filt1000GALL) threshold_1000g_ALL=$2;shift;; #threshold value 240 --filt1000GALL) threshold_1000g_ALL=$2;shift;; #threshold value
240 --filt1000GAFR) threshold_1000g_AFR=$2;shift;; #threshold value 241 --filt1000GAFR) threshold_1000g_AFR=$2;shift;; #threshold value