alter annotation db

tasks/annovar.wdl

@@ -14,14 +14,14 @@ task annovar {
     set -e
     nt=$(nproc)
 
-    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
+    #awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
 
     if [ ${hg} == "hg38" ]; then
-    /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
+    /installations/annovar/table_annovar.pl ${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 \
+    -protocol refGene,ensGene,knownGene,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,dbscsnv11,dbnsfp31a_interpro,exac03,gnomad211_exome,cosmic92_coding,cosmic92_noncoding \
+    -operation g,g,g,r,r,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f \
     -nastring . -vcfinput -thread $nt
     fi
 
@@ -49,7 +49,6 @@ 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"