summary

tasks/region.wdl

@@ -54,11 +54,12 @@ task region {
 
 		for i in *vcf.gz
 		do
-			cat $i | grep -v '#' >> ${sample_name}.${tag}.all.count.txt
-			cat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample_name}.${tag}.snv.mc.count.txt
-			cat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.snv.mc.same.genotype.count.txt
-			cat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample_name}.${tag}.indel.mc.count.txt
-			cat $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
+			zcat $i | grep -v '#' | grep 'SNV' >> ${sample_name}.${tag}.all.snv.count.txt
+			zcat $i | grep -v '#' | grep 'INDEL' >> ${sample_name}.${tag}.all.indel.count.txt
+			zcat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample_name}.${tag}.snv.mc.count.txt
+			zcat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.snv.mc.same.genotype.count.txt
+			zcat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample_name}.${tag}.indel.mc.count.txt
+			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
 
 		ls *vcf.gz > file.list.txt
@@ -99,6 +100,7 @@ task region {
 		File indel = "${sample_name}.${tag}.indel.mc.count.txt"
 		File indel_mc = "${sample_name}.${tag}.indel.mc.same.genotype.count.txt"
 		File file_list = "file.list.txt"
-		File all = "${sample_name}.${tag}.all.count.txt"
+		File all_snv = "${sample_name}.${tag}.all.snv.count.txt"
+		File all_indel = "${sample_name}.${tag}.all.indel.count.txt"
 	}
 }