1 changed files with 4 additions and 1 deletions
+ 4
- 1
tasks/bcftools.wdl
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| bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz | 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 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 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 merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ | ||||
| bcftools plugin fill-AN-AC |\ | bcftools plugin fill-AN-AC |\ | ||||
| bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf | ||||
| else | else | ||||
| touch panel_of_normal.vcf | touch panel_of_normal.vcf | ||||
| fi | fi |
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