1 changed files with 6 additions and 6 deletions
+ 6
- 6
tasks/bcftools.wdl
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| if [ ${PONmode} ]; then | if [ ${PONmode} ]; then | ||||
| mkdir -p /cromwell_root/tmp/bcftools/ | mkdir -p /cromwell_root/tmp/bcftools/ | ||||
| cp ${pon_vcf1} /cromwell_root/tmp/bcftools/ | |||||
| bcftools view /cromwell_root/tmp/bcftools/${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz | |||||
| cp ${pon_vcf2} /cromwell_root/tmp/bcftools/ | |||||
| bcftools view /cromwell_root/tmp/bcftools/${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz | |||||
| cp ${pon_vcf3} /cromwell_root/tmp/bcftools/ | |||||
| bcftools view /cromwell_root/tmp/bcftools/${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf3}.gz | |||||
| bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz | |||||
| bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz | |||||
| bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${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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