trio

tasks/merge_mendelian.wdl

@@ -15,13 +15,13 @@ 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 > ${family_name}.inside.D5.txt
+		cat ${family_name}.inside.txt | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.inside.D5.txt
 
-		cat ${family_name}.inside.txt | cut -f12 | cut -d: -f3 > ${family_name}.inside.D6.txt
+		cat ${family_name}.inside.txt | cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.inside.D6.txt
 
-		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f2 > ${family_name}.outside.D5.txt
+		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f2 | sort | uniq -c > ${family_name}.outside.D5.txt
 
-		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f3 > ${family_name}.outside.D6.txt
+		cat ${family_name}.outside.txt | cut -f12 | cut -d: -f3 | sort | uniq -c > ${family_name}.outside.D6.txt
 	>>>
 
 	runtime {