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malthesr / winsfs

Site frequency spectrum estimation based on window expectation-maximisation algorithm
MIT License
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Determining FST based on winSFS output #10

Closed chrishusted closed 8 months ago

chrishusted commented 10 months ago

Hi there,

Thank you for implementing a much faster SFS method! I was just curious if you have suggestions for performing FST using the winSFS ouput. Will it work with the angsd implementation?

Best, Chris

chrishusted commented 10 months ago

It appears as though the answer is that you need to remove the header, but you can run the ANGSD FST calculation after doing so.

malthesr commented 9 months ago

Hi Chris,

Sorry for the slow reply.

I haven't used the Fst stuff in ANGSD for a while, so I'm not sure about the details, but as you say, the output format of winsfs is the same as the one used in ANGSD, except it adds a header with the dimensions. So if all you need is an estimate of the SFS, you should be good to go by just removing the header.

chrishusted commented 8 months ago

Apologies for taking so long to respond! This worked and I greatly appreciate the support.