Update: rmsk

tasks/annovar.wdl

@@ -22,15 +22,7 @@ task annovar {
     -operation r \
     -nastring . -vcfinput -thread $nt
     fi
-
-    if [ ${hg} == "hg19" ]; then
-    /installations/annovar/table_annovar.pl ${vcf}\
-    ${annovar_database} -buildver ${hg} \
-    -out ${basename} -remove \
-    -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 \
-    -operation g,r,r,f,f,f,f,f,f \
-    -nastring . -vcfinput -thread $nt
-    fi
+    
   >>>
   
   runtime {