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tasks/annovar.wdl
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| @@ -13,8 +13,8 @@ task annovar { | |||
| set -o pipefail | |||
| set -e | |||
| nt=$(nproc) | |||
| /installations/annovar/table_annovar.pl ${TNscope_vcf} ${database} -buildver hg38 -out ${sample}_TNscope -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| /installations/annovar/table_annovar.pl ${TNseq_vcf} ${database} -buildver hg38 -out ${sample}_TNseq -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| /installations/annovar/table_annovar.pl ${TNscope_vcf} ${database} -buildver hg38 -out ${sample}.TNscope -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| /installations/annovar/table_annovar.pl ${TNseq_vcf} ${database} -buildver hg38 -out ${sample}.TNseq -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| >>> | |||
| runtime { | |||
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