更新 'tasks/bcftools_concat.wdl'

tasks/bcftools_concat.wdl

@@ -14,8 +14,12 @@ task bcftools {
     set -e
     nt=$(nproc)
     
-    bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}_stralka.vcf.gz
-    bcftools index -t ${sample_id}_stralka.vcf.gz
+    bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}.strelka.vcf.gz          
+    bcftools norm -m -both ${sample_id}.strelka.vcf.gz -O z -o ${sample_id}.strelka.norm.vcf.gz
+    bcftools view -O z -f 'PASS' ${sample_id}.strelka.norm.vcf.gz -o ${sample_id}.strelka.PASS.vcf.gz
+    bcftools index -t ${sample_id}.strelka.PASS.vcf.gz
+           
+    ls ./
 
   >>>
   
@@ -27,7 +31,7 @@ task bcftools {
   }
   
   output {
-    File concat_vcf = "${sample_id}_stralka.vcf.gz"
-    File concat_vcf_index = "${sample_id}_stralka.vcf.gz.tbi"
+    File concat_vcf = "${sample_id}.strelka.PASS.vcf.gz"
+    File concat_vcf_index = "${sample_id}.strelka.PASS.vcf.gz.tbi"
   }
 }