snv_indel

tasks/merge_mendelian.wdl

@@ -15,13 +15,21 @@ task merge_mendelian {
 
 		python /opt/merge_two_family_with_genotype.py -LCL5 ${D5_out} -LCL6 ${D6_out} -genotype ${family_out} -family ${family_name}.outside
 
-		cat ${family_name}.inside.txt | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.inside.D5.txt
+		cat ${family_name}.inside.txt | grep SNV | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.inside.D5.snv.txt
 
-		cat ${family_name}.inside.txt | cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.inside.D6.txt
+		cat ${family_name}.inside.txt | grep INDEL | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.inside.D5.indel.txt
 
-		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.outside.D5.txt
+		cat ${family_name}.inside.txt | grep SNV |cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.inside.D6.snv.txt
 
-		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.outside.D6.txt
+		cat ${family_name}.inside.txt | grep INDEL |cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.inside.D6.indel.txt
+
+		cat ${family_name}.outside.txt | grep SNV |cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.outside.D5.snv.txt
+
+		cat ${family_name}.outside.txt | grep INDEL |cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.outside.D5.indel.txt
+
+		cat ${family_name}.outside.txt | grep SNV |cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.outside.D6.snv.txt
+
+		cat ${family_name}.outside.txt | grep INDEL |cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.outside.D6.indel.txt
 	>>>
 
 	runtime {
@@ -35,9 +43,14 @@ task merge_mendelian {
 		File mendelian_in_summary = "${family_name}.inside.summary.txt"
 		File mendelian_out = "${family_name}.outside.txt"
 		File mendelian_out_summary = "${family_name}.outside.summary.txt"
-		File D5_inside = "${family_name}.inside.D5.txt"
-		File D5_outside = "${family_name}.outside.D5.txt"
-		File D6_inside = "${family_name}.inside.D6.txt"
-		File D6_outside = "${family_name}.outside.D6.txt"
+		File D5_snv_inside = "${family_name}.inside.D5.snv.txt"
+		File D5_indel_inside = "${family_name}.inside.D5.indel.txt"
+		File D6_snv_inside = "${family_name}.inside.D6.snv.txt"
+		File D6_indel_inside = "${family_name}.inside.D6.indel.txt"
+		File D5_snv_outside = "${family_name}.outside.D5.snv.txt"
+		File D5_indel_outside = "${family_name}.outside.D5.indel.txt"
+		File D6_snv_outside = "${family_name}.outside.D6.snv.txt"
+		File D6_indel_outside = "${family_name}.outside.D6.indel.txt"
+
 	}
 }