HGVS

tasks/annovar.wdl

@@ -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 {