Update: annovar

tasks/ANNOVAR.wdl

@@ -22,11 +22,21 @@ task ANNOVAR {
     fi
 
     if [ ${hg} == "hg38" ]; then
-      /installations/annovar/table_annovar.pl INPUT.vcf ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+    /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
+    ${annovar_database} -buildver ${hg} \
+    -out ${basename} -remove \
+    -protocol refGene,ensGene,knownGene,rmsk,cytoBand,genomicSuperDups,esp6500siv2_all,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \
+    -operation g,g,g,r,r,r,f,f,f,f,f,f,f,f,f,f,f,f,f \
+    -nastring . -vcfinput -thread $nt
     fi
 
     if [ ${hg} == "hg19" ]; then
-      /installations/annovar/table_annovar.pl INPUT.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
+    /installations/annovar/table_annovar.pl ${basename}.PASS.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
   >>>