ti_tv

tasks/region.wdl

@@ -62,6 +62,19 @@ task region {
 			zcat $i | grep -v '#' | grep 'INDEL;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.indel.mc.same.genotype.count.txt
 		done
 
+
+		for i in *vcfstat.txt
+		do
+			cat $i | sed -n '13,13p' | sed 's/\s\+/\t/g' | cut -f3 >> ${sample_name}.${tag}.ti_tv.txt
+		done
+
+
+		for i in *vcfstat.txt
+		do
+			cat $i | sed -n '14,14p' | sed 's/\s\+/\t/g' | cut -f5 >> ${sample_name}.${tag}.het_hom.txt
+		done		
+
+
 		ls *vcf.gz > file.list.txt
 
 
@@ -102,5 +115,7 @@ task region {
 		File file_list = "file.list.txt"
 		File all_snv = "${sample_name}.${tag}.all.snv.count.txt"
 		File all_indel = "${sample_name}.${tag}.all.indel.count.txt"
+		File ti_tv = "${sample_name}.${tag}.ti_tv.txt"
+		File het_homo = "${sample_name}.${tag}.het_hom.txt"
 	}
 }