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Calculate the Fst between populations

Hello,

I want to find the difference between some populations in my data, so I can find which of them is or are the most ancient population to be categorized as the ancestry population. After getting .Q file and .P file from ADMIXTURE and plot, I don't know if I need to calculate Fst or something else, if so, How can I get the Fst table that I have seen in some papers?

Thank you

snp gene sequence
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updated by Ram Ram • written by dirranrak • dirranrak

1 answer

If you used Admixture your input files should be in Plink format. In this case you can use plink directly with the --fst option.

In alternative, if your files are vcf, you can calculate fst using vcftools.

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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Ok, here my are Options in effect:

    --bfile trialmergedexcludedrs3926405,rs365066AfricaKhoisanexcludedsnpwith0phenotypegeno0.05hwe0.001Batwa_Kiga.913651pos.230samples.PNAS2014_trial1_flip
    --fst
    --within trialmergedexcludedrs3926405,rs365066AfricaKhoisanexcludedsnpwith0phenotypegeno0.05hwe0.001Batwa_Kiga.913651pos.230samples.PNAS2014_trial1_flip.5.P
    --out Fstpopremoved

and I have got results and don't seem like a Fst table but .hh, .nosex and the .log file.

• 0 views • link
updated by Ram Ram • written by dirranrak • dirranrak

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