How to generate a smoothing plot for Fst along the genome from Lositan output?

Question

[Anurag]

Hi All,

I want to make a genome wide Fst plot using the Lositan output along with P-Values calculated by lositan.

Any inputs will be appreciated.

Thanks

Answer 1

[Zev.Kronenberg]

I don't know how to do it from Lositan, but I have all the details how to do it using my code:

https://github.com/jewmanchue/vcflib/wiki

Check out the library, run wcFst:

https://github.com/jewmanchue/vcflib/wiki/Association-testing-with-GPAT

smooth it:

https://github.com/jewmanchue/vcflib/wiki/Smoothing-with-GPAT