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.
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.
Do those sites have a low allele frequency?
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.