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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
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kSFS #15

Closed barlavi1 closed 3 years ago

barlavi1 commented 3 years ago

Hi, I am trying to construct the kSFS table in order to use it as an input for MUSHI. I'm using 10 homozygous samples and the resulting sfs matrix has 19 rows, when rows 1,3,5,7,9,..,19 are all zeros. Is that a logical output?

Thanks, Bar

wsdewitt commented 3 years ago

Hi Bar,

The rows correspond to allele frequencies, so if all the variants in your VCF are homozygous, they will have even-numbered allele frequencies in the sample, and the odd rows will contain zeros. I'll follow up via email to ask more about your use case.

-- Will