first commit

tasks/bcftools.wdl

@@ -19,10 +19,7 @@ task bcftools {
 			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			cd /cromwell_root/tmp/bcftools
-			for i in `ls *.gz`
-			do
-			bcftools index $i
-			done
+			for i in `ls *.gz`; do bcftools index $i -f; 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