Update: filtering PASS

tasks/annovar.wdl

@@ -14,17 +14,21 @@ task annovar {
     set -e
     nt=$(nproc)
 
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
+
     if [ ${hg} == "hg38" ]; then
-    /installations/annovar/table_annovar.pl ${vcf} \
+    /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,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
 
     if [ ${hg} == "hg19" ]; then
-    /installations/annovar/table_annovar.pl ${vcf} \
+    /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 \
@@ -41,6 +45,7 @@ task annovar {
   }
 
   output {
+    File pass_vcf = "${basename}.PASS.vcf"
     File avinput = "${basename}.avinput"
     File multianno_txt = "${basename}.${hg}_multianno.txt"
     File multianno_vcf = "${basename}.${hg}_multianno.vcf"