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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

can pixy be used in haploid species #65

Closed wushyer closed 1 year ago

wushyer commented 1 year ago

Hi could I ask if pixy can be used in the haploid species? Thanks Best Shuangyang

ksamuk commented 1 year ago

Not currently, but this is a planned feature!

wushyer commented 1 year ago

But I tried it on my haploid genome and it works! The value is similar with the modified haploid mode vcftools.

Kieran Samuk @.***>于2022年12月12日 周一18:17写道：

Not currently, but this is a planned feature!

— Reply to this email directly, view it on GitHub https://github.com/ksamuk/pixy/issues/65#issuecomment-1346995584, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFAWWO6TQIU3G5XNP6KQY7LWM5T5FANCNFSM6AAAAAAQ4RBVOM . You are receiving this because you authored the thread.Message ID: @.***>

ksamuk commented 1 year ago

That's good to hear, but in order for this to be fully supported, we will need to carefully validate the computed values via simulations etc., in the same way we did for diploid data. I'd avoid using it for haploid species for now, personally!