更新 'tasks/bcftools.wdl'

tasks/bcftools.wdl

@@ -16,6 +16,7 @@ task bcftools {
     # bcftools norm -m -both ${vcf} | bcftools norm -f ${ref_dir}/${fasta} -Ov -o ${basename}.norm.vcf
     # Split multiallelic sites
     bcftools norm -m -both ${vcf} -o ${basename}.norm.vcf
+    bcftools view -O z -f 'PASS' ${basename}.norm.vcf -o ${basename}.PASS.vcf.gz
   >>>
   
   runtime {
@@ -26,6 +27,6 @@ task bcftools {
   }
   
   output {
-    File norm_vcf = "${basename}.norm.vcf"
+    File norm_vcf = "${basename}.PASS.vcf.gz"
   }
 }