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Is there a way to phase an unphased data for selection detection?

Hi!

I have ped/map file containing two populations (~110 samples, ~500k SNPs). Is there a software which can phase the data? Alleles should be coded as 1 and 0, where 0 reflects ancestral allele.

I am trying to detect selection and at the moment preparing an input file for selscan programm. So if you can suggest good alternative programs it will help as well.

Thanks.

snp ped phase unphased selection
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updated by Ram Ram • written by eyb eyb

1 answer

Was the data in VCF format before plink? There are lots of ways to phase in VCF. BEAGLE is my preferred phasing algorithm.

Also if your are interested, I have been writing selection software that works directly from VCF.

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

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

Thanks. I have converted my data to VCF and ran beagle on it. Is reduction of SNP numbers is normal? I am missing 2/3 of my SNPs.

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written by eyb eyb

Do those sites have a low allele frequency?

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

I figured out what was the problem. I didn't clear the file from VG type of SNPs so beagle was stopping half way through.

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written by eyb eyb

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