Determining FST based on winSFS output

[chrishusted]

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]

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]

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]

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