Question: Is there a way to phase an unphased data for selection detection?
1
gravatar for eyb
5.2 years ago by
eyb180
Russian Federation
eyb180 wrote:

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.

unphased ped selection phase snp • 2.1k views
ADD COMMENTlink modified 5.2 years ago by Zev.Kronenberg11k • written 5.2 years ago by eyb180
6
gravatar for Zev.Kronenberg
5.2 years ago by
United States
Zev.Kronenberg11k wrote:

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 COMMENTlink modified 5.2 years ago • written 5.2 years ago by Zev.Kronenberg11k

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 REPLYlink written 5.2 years ago by eyb180

Do those sites have a low allele frequency?  

ADD REPLYlink written 5.2 years ago by Zev.Kronenberg11k
1

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 REPLYlink written 5.2 years ago by eyb180
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