first commit

tasks/bcftools.wdl

@@ -26,9 +26,7 @@ task bcftools {
 			#bcftools index FUSCCTNBC330_pon.vcf.gz
 			#bcftools index FUSCCTNBC467_pon.vcf.gz
 
-			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
+			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