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Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids)

Open taprs opened this issue 1 year ago • 1 comments

Thank you for this tool! The idea is pretty elegant and we have been needing the "official" script to do these simple stats for so long...

I understand that this was likely addressed in #79 but I want it to be said explicitly : we would like to see arbitrary ploidy level support! From our test runs it seems that pixy silently takes first two alleles in polyploids and thus dramatically lowers the pi estimate for polyploids.

It would be good, as a first quick fix, to add a warning (or maybe even an error?) if any cells of the input VCF have ploidy other than 2. Then I have a dream of being able to use pixy with arbitrary ploidy level, including cases when different samples or genomic positions have different ploidy levels...

Best wishes, Nikita

taprs avatar Jan 24 '24 18:01 taprs