Is there a way to phase an unphased data for selection detection?
1
1
Entering edit mode
7.0 years ago
eyb ▴ 220

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 • 2.7k views
ADD COMMENT
6
Entering edit mode
7.0 years ago

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

 

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Do those sites have a low allele frequency?  

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2544 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6