test rmsk

tasks/annovar.wdl

@@ -14,13 +14,15 @@ 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}\
-    ${annovar_database} -buildver ${hg} \
-    -out ${basename} -remove \
-    -protocol rmsk \
-    -operation r \
-    -nastring . -vcfinput -thread $nt
+      /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
+      ${annovar_database} -buildver ${hg} \
+      -out ${basename} -remove \
+      -protocol rmsk,exac03,gnomad211_exome,cosmic92_coding,cosmic92_noncoding \
+      -operation r,f,f,f,f \
+      -nastring . -vcfinput -thread $nt
     fi
     
   >>>