Created wdl to split cnvs into del / dup records

Author: kjaisingh

wdl/ExtractCnvsFromVcf.wdl

@@ -0,0 +1,77 @@
+version 1.0
+
+workflow ExtractCnvsFromVcf {
+	input {
+		File vcf               # Input VCF
+		File vcf_idx           # Input VCF index file
+
+		String gatk_docker     # Docker image path for GATK
+	}
+	
+	call ExtractCnvs {
+		input:
+			vcf  					= vcf,
+			vcf_idx 	    = vcf_idx
+	}
+
+	output {
+		File extracted_vcf	 		= ExtractCnvs.extracted_vcf
+		File extracted_vcf_idx 	= ExtractCnvs.extracted_vcf_idx
+	}
+}
+
+task ExtractCnvs {
+	input {
+		File vcf
+		File vcf_idx
+		String gatk_docker
+	}
+
+	command <<<
+		set -eu -o pipefail
+
+		python <<CODE
+import pysam
+import copy
+
+fin = pysam.VariantFile("~{vcf}")
+fout = pysam.VariantFile("extracted.vcf", 'w', header=fin.header)
+
+for rec in fin:
+	if rec.info.get("SVTYPE") == "CNV":
+		rec_del = copy.copy(rec)
+		rec_del.id = rec.id + "_DEL"
+		rec_del.info["SVTYPE"] = "DEL"
+		rec_del.alts = ("<DEL>",)
+		
+		rec_dup = copy.copy(rec)
+		rec_dup.id = rec.id + "_DUP"
+		rec_dup.info["SVTYPE"] = "DUP"
+		rec_dup.alts = ("<DUP>",)
+		
+		fout.write(rec_del)
+		fout.write(rec_dup)
+	else:
+		fout.write(rec)
+
+fin.close()
+fout.close()
+CODE
+
+			bgzip extracted.vcf
+
+			tabix extracted.vcf.gz
+    >>>
+
+	output {
+		File extracted_vcf = "extracted.vcf.gz"
+		File extracted_vcf_idx = "extracted.vcf.gz.tbi"
+	}
+
+	runtime {
+		cpu: 1
+		memory: "4 GiB"
+		disks: "local-disk 4 HDD"
+		docker: gatk_docker
+	}
+}