search

Amine-Namouchi / snpToolkit

GNU General Public License v3.0
4 stars 0 forks source link

Add outgroup option to snptoolkit combine? #5

Open Kelzor opened 3 years ago

Kelzor commented 3 years ago

This is not an issue, but a request/suggestion.

Would it be possible to add an outgroup masking feature to snptoolkit combine? For example, the outgroup is processed along with the study samples and included in the combine command like the study samples via VCF and bam files, but it is specified with an --outgroup flag and only SNP positions called in the study samples get called in the outgroup sample for the multiple sequence SNP alignment. The alignment size can get very large in studies with highly divergent outgroups, so this would help with tree building efficiency.

Cheers, Kelly

Amine-Namouchi commented 3 years ago

Very good suggestion, will not be a big deal to implement it. I will let you know when this is done