summary

tasks/region.wdl

@@ -52,6 +52,17 @@ task region {
 		rtg vcfstat ${sample_name}.${tag}.del_breakpoint.vcf.gz > ${sample_name}.${tag}.del_breakpoint.vcfstat.txt
 		rtg vcfstat ${sample_name}.${tag}.mhc.vcf.gz > ${sample_name}.${tag}.mhc.vcfstat.txt
 
+		for i in *vcf.gz
+		do
+			cat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample}.${tag}.snv.mc.count.txt
+			cat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample}.${tag}.snv.mc.same.genotype.count.txt
+			cat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample}.${tag}.indel.mc.count.txt
+			cat $i | grep -v '#' | grep 'INDEL;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample}.${tag}.indel.mc.same.genotype.count.txt
+		done
+
+		ls *vcf.gz > file.list.txt
+
+
 
 	>>>
 
@@ -82,5 +93,10 @@ task region {
 		File ins_breakpoint_stat = "${sample_name}.${tag}.ins_breakpoint.vcfstat.txt"
 		File del_breakpoint_stat = "${sample_name}.${tag}.del_breakpoint.vcfstat.txt"
 		File mhc_stat = "${sample_name}.${tag}.mhc.vcfstat.txt"
+		File snv = "${sample}.${tag}.snv.mc.count.txt"
+		File snv_mc = "${sample}.${tag}.snv.mc.same.genotype.count.txt"
+		File indel = "${sample}.${tag}.indel.mc.count.txt"
+		File indel_mc = "${sample}.${tag}.indel.mc.same.genotype.count.txt"
+		File file_list = "file.list.txt"
 	}
 }