first commit

tasks/bcftools.wdl

@@ -14,21 +14,22 @@ task bcftools {
 		set -e
 		
 		if [ ${PONmode} ]; then
-			mkdir -p /cromwell_root/tmp/bcftools/
+			mkdir -p /cromwell_root/tmp/bcftools
 			
-
 			bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			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
-			bcftools index *.vcf.gz
+			#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