1 değiştirilmiş dosya ile 3 ekleme ve 2 silme
+ 3
- 2
tasks/bcftools.wdl
Dosyayı Görüntüle
| 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 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/*.vcf.gz | |||||
| cd /cromwell_root/tmp/bcftools | |||||
| bcftools index *.vcf.gz | |||||
| bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ | |||||
| bcftools merge -m all -f PASS,. --force-samples *.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 | ||||
Yükleniyor…