first commit

tasks/bcftools.wdl

@@ -25,9 +25,11 @@ task bcftools {
 			bcftools index *.vcf.gz
 			#bcftools index FUSCCTNBC330_pon.vcf.gz
 			#bcftools index FUSCCTNBC467_pon.vcf.gz
-
+			for i in ${sep=" " *.vcf.gz}
+			do
+			bcftools index $i
+			done
 			bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
-
 		else
 			touch panel_of_normal.vcf
 		fi