Update: annovar

tasks/annovar.wdl

@@ -20,12 +20,13 @@ task annovar {
     /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
     ${annovar_database} -buildver ${hg} \
     -out ${basename} -remove \
-    #-protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20210501 \
-    #-operation g,r,r,f,f,f,f,f,f,f \
     -protocol refGene,ensGene,knownGene,rmsk,esp6500siv2_all,1000g2015aug,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \
     -operation g,g,g,r,f,f,f,f,f,f,f,f \
     -nastring . -vcfinput -thread $nt
     fi
+    
+    #-protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20210501 \
+    #-operation g,r,r,f,f,f,f,f,f,f \
 
     if [ ${hg} == "hg19" ]; then
     /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \