summary

tasks/region.wdl

 
 		for i in *vcf.gz
 		do
+			cat $i | grep -v '#' >> ${sample}.${tag}.all.count.txt
 			cat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample}.${tag}.snv.mc.count.txt
 			cat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample}.${tag}.snv.mc.same.genotype.count.txt
 			cat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample}.${tag}.indel.mc.count.txt
 		File indel = "${sample}.${tag}.indel.mc.count.txt"
 		File indel_mc = "${sample}.${tag}.indel.mc.same.genotype.count.txt"
 		File file_list = "file.list.txt"
+		File all = "${sample}.${tag}.all.count.txt"
 	}
 }