1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/bcftools.wdl
View File
| mkdir -p /cromwell_root/tmp/bcftools/ | mkdir -p /cromwell_root/tmp/bcftools/ | ||||
| bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz | |||||
| bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools | |||||
| bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz | |||||
| bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools | |||||
| bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf3}.gz | |||||
| bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools | |||||
| 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 |\ |
Loading…