1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/bcftools.wdl
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| mkdir -p /cromwell_root/tmp/bcftools/ | mkdir -p /cromwell_root/tmp/bcftools/ | ||||
| bcftools view ${pon_vcf1} -Oz -o /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 | |||||
| bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz | |||||
| bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/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 any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ | ||||
| bcftools plugin fill-AN-AC |\ | bcftools plugin fill-AN-AC |\ |
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