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Permutation of Fst statistics of genotyped data to get p value

Hello, I have genotyped data of two populations in plink format. I need to do permutation to calculate Fst to obtain empirical p values. Plink doesn't have the provision to do it for Fst. Can you please help me with a software and method to do so? I've been trying to do this for over a month and getting quite frustrated since I'm not able to find a correct way to do this.

Regards.

genotype fst plink pvalue empirical pvalue
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updated by pooja.singh09 • pooja.singh09 • written by doodle • doodle

1 answer

https://github.com/rnowling/fst-permutation-tests

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written by pooja.singh09 • pooja.singh09

Thank you so much Pooja! I hadn't noticed your reply earlier. I'll try this and get back to you.

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written by doodle • doodle

@pooja.singh09 ... I have been trying to run permutation for fst from the link you sent. I'm running into errors. Have you used it before? If yes, can you help me with the error if I put them up here?

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written by doodle • doodle

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