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tasks/bcftools.wdl
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| @@ -18,15 +18,18 @@ task bcftools { | |||
| bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz | |||
| bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz | |||
| bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz | |||
| bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz | |||
| bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz | |||
| bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).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 | |||
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