filter vcf

tasks/VQSR.wdl

@@ -52,6 +52,10 @@ command <<<
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo ApplyVarCal -v ${sample}.vqsrSNP.hc.recaled.vcf.gz --var_type INDEL --recal ${sample}.vqsrINDEL.hc.recal --tranches_file ${sample}.vqsrINDEL.hc.tranches --sensitivity 99.0 ${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz
 		${SENTIEON_INSTALL_DIR}/bin/sentieon plot vqsr -o ${sample}.vqsrINDEL.VQSR.pdf ${sample}.vqsrINDEL.hc.plotfile
 
+		zcat ${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz | grep '#' > header
+		zcat ${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz | grep -v '#' | grep PASS > body
+		cat header body > ${sample}.vqsrSNPINDEL.hc.recaled.pass.vcf
+
 	>>>
 	
 	runtime {
@@ -62,7 +66,8 @@ command <<<
 	}
 
 	output {
-	File filtered_vcf = "${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz"
+	File masked_vcf = "${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz"
+	File filtered_vcf = "${sample}.vqsrSNPINDEL.hc.recaled.pass.vcf"
 	}
 }