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tasks/annovar.wdl
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| @@ -10,7 +10,7 @@ task annovar { | |||
| command <<< | |||
| nt=$(nproc) | |||
| /installations/annovar/table_annovar.pl ${vcf_file} ${database} -buildver hg19 -out ${sample} -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20190305,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| /installations/annovar/table_annovar.pl ${vcf_file} ${database} -buildver hg19 -hgvs -out ${sample} -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20190305,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| >>> | |||
| runtime { | |||
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