ped file

tasks/mendelian.wdl

@@ -11,18 +11,14 @@ task mendelian {
 		export LD_LIBRARY_PATH=/opt/htslib-1.9
 		nt=$(nproc)
 
-		echo "${chromo}	LCL8_consensus_call	0	0	2	-9
-		${chromo}	LCL7_consensus_call	0	0	1	-9
-		${chromo}	LCL5_consensus_call	LCL7_consensus_call	LCL8_consensus_call	2	-9" > ${chromo}.D5.ped
+		echo -e "${chromo}\tLCL8_consensus_call\t0\t0\t2\t-9\n${chromo}\tLCL7_consensus_call\t0\t0\t1\t-9\n${chromo}\tLCL5_consensus_call\tLCL7_consensus_call\tLCL8_consensus_call\t2\t-9" > ${chromo}.D5.ped
 
 		mkdir VBT_D5
 		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${consensus_vcf} -father ${consensus_vcf} -child ${consensus_vcf} -pedigree ${chromo}.D5.ped -outDir VBT_D5 -out-prefix ${chromo}.D5 --output-violation-regions -thread-count $nt
 
 		cat VBT_D5/${chromo}.D5_trio.vcf > ${chromo}.D5.vcf
 
-		echo "${chromo}	LCL8_consensus_call	0	0	2	-9
-		${chromo}	LCL7_consensus_call	0	0	1	-9
-		${chromo}	LCL6_consensus_call	LCL7_consensus_call	LCL8_consensus_call	2	-9" > ${chromo}.D6.ped
+		echo -e "${chromo}\tLCL8_consensus_call\t0\t0\t2\t-9\n${chromo}\tLCL7_consensus_call\t0\t0\t1\t-9\n${chromo}\tLCL6_consensus_call\tLCL7_consensus_call\tLCL8_consensus_call\t2\t-9" > ${chromo}.D6.ped
 
 		mkdir VBT_D6
 		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${consensus_vcf} -father ${consensus_vcf} -child ${consensus_vcf} -pedigree ${chromo}.D6.ped -outDir VBT_D6 -out-prefix ${chromo}.D6 --output-violation-regions -thread-count $nt
@@ -45,4 +41,7 @@ task mendelian {
 		File D6_trio_vcf = "${chromo}.D6.vcf"
 		File family_vcf = "${chromo}.vcf"
 	}
-}
+}
+
+
+