count number

tasks/region.wdl

@@ -54,8 +54,8 @@ task region {
 
 		for i in *vcf.gz
 		do
-			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' | wc -l >> ${sample_name}.${tag}.all.snv.count.txt
+			zcat $i | grep -v '#' | grep 'INDEL'| wc -l >> ${sample_name}.${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