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

Question

[eyb]

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.

Answer 1

[Zev.Kronenberg]

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

[eyb]

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.

[Zev.Kronenberg]

Do those sites have a low allele frequency?

[eyb]

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.