Question: How to calculate IBD for different ethnicity using plink
0
gravatar for MAPK
3.8 years ago by
MAPK1.5k
MAPK1.5k wrote:

I have a multigenome vcf file with samples from different ethnicities. I have converted this file to .ped and .map formats to work with Plink. I want to calculate the IBD relationship of samples using Plink, but I don't know exactly how it works and how it takes the problem of population stratification into account while calculating IBD. Can someone please explain a bit on this. Thanks

ibd plink • 1.6k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by MAPK1.5k

I don't think plink will take population stratification into account. You will have to adjust for it by carrying out population stratification analysis and isolating your population of interest. Plink can be used to carry out the population stratification (http://pngu.mgh.harvard.edu/~purcell/plink/strat.shtml) or you could also use SNPRelate (http://bioconductor.org/packages/release/bioc/vignettes/SNPRelate/inst/doc/SNPRelateTutorial.html)

ADD REPLYlink written 3.8 years ago by vakul.mohanty240

Thanks! Do you know how many SNPs Plink needs?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by MAPK1.5k

I'm not sure. You could write to the authors they might be able to give you more concrete answers.

ADD REPLYlink written 3.8 years ago by vakul.mohanty240
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 856 users visited in the last hour