Since genmod only considers the chromosome and position, the sort is unstable for variants that share the same chromosome and position. Could consider implementing sorting also on REF+ALT like bcftools sort (compared lexicographically as a tab-separated string, used as a tiebreaker when CHROM and POS are equal).
Alternatives:
- Drop multiprocessing
- Use
bcftools sort instead of sort internally
Since genmod only considers the chromosome and position, the sort is unstable for variants that share the same chromosome and position. Could consider implementing sorting also on REF+ALT like bcftools sort (compared lexicographically as a tab-separated string, used as a tiebreaker when CHROM and POS are equal).
Alternatives:
bcftools sortinstead of sort internally