Running winSFS on a region

[msrigyan]

Hi,

I am wondering if it is possible to run winSFS on a particular chromosome/region, if the saf files are already generated? I want to examine the SFS for a single region from the saf.idx file for the whole genome.

Previously, I did this using realSFS with the command:
$angsd/misc/realSFS $file.saf.idx -r $chr1 > $chr1.sfs

If there's a way to do this using winsfs, that would be really helpful, thank you!

[malthesr]

Hi,

Depending on what you need to do, some of the discussion here might be relevant.

Apart from that, the only way would be to to generate SAF files separately by regions and run winsfs by those. In any case, be aware that winsfs is intended for use on large input data, so you'd want to keep the separate input blocks large (in the 10s-100s of mb, at least). For smaller blocks, realSFS would be the better choice.

Best,
Malthe