+ bcftools --version
bcftools 1.22
Using htslib 1.22.1
Copyright (C) 2025 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
+ echo 'Hard filtering variants'
Hard filtering variants
+ bcftools filter -e 'QUAL < 30.0 || FMT/DP < 10 || FMT/GQ < 20 || FMT/DP > 150 || FMT/AF1 < 0.3' --soft-filter FAIL -Oz -o Ptua.biscuit.merged-filtered.vcf.gz Ptua.biscuit.merged.vcf.gz
+ bcftools index Ptua.biscuit.merged-filtered.vcf.gz
+ echo 'Selecting SNPs that pass fitering'
Selecting SNPs that pass fitering
+ bcftools view -f PASS Ptua.biscuit.merged-filtered.vcf.gz -Oz -o Ptua.biscuit.merged-filtered-true.vcf.gz
[2025-07-28T19:40:06.229] error: unable to open '/proc/99693/cgroup' for reading : No such file or directory
+ bcftools view -i '(32-COUNT(GT="mis"))/32>=0.8' -m2 -M2 Ptua.biscuit.merged-filtered-true.vcf.gz -o Ptua.biscuit.merged-filtered-true-all.vcf.gz