first commit

tasks/bcftools.wdl

@@ -23,9 +23,10 @@ task bcftools {
 
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
 
-			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
+			bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\ 
 			bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
+			
 		else
 			touch panel_of_normal.vcf
 		fi