Question: Calculate the Fst between populations
0
gravatar for dirranrak
3.5 years ago by
dirranrak10
United States
dirranrak10 wrote:

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 sequence gene • 3.1k views
ADD COMMENTlink modified 3.5 years ago by Giovanni M Dall'Olio26k • written 3.5 years ago by dirranrak10
1
gravatar for Giovanni M Dall'Olio
3.5 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Giovanni M Dall'Olio26k

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.

ADD REPLYlink written 3.5 years ago by dirranrak10
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