Question: Imputation and haplotype phasing in Bovine 50K SNP data
gravatar for kas
7 weeks ago by
kas0 wrote:

Hello everyone, I'm new to this haplotype phasing and imputation. I have plink output files (.ped, .map, .bed, .vcf). I don't know how to proceed further. If anybody using Beagle or shapeit for Bovine 50K SNP data, please help me. And also list any software that can be used to make .hap files.

snp chip-seq software error • 127 views
ADD COMMENTlink written 7 weeks ago by kas0

What is the aim of your analysis? Why do you have chip-seq and software error as tags?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Kevin Blighe50k

My aim is to do haplotype phasing using Bovine 50K chip data (in plink format). I'm asking the method to proceed further

ADD REPLYlink written 6 weeks ago by kas0

You may want to take a look at this technical report: Haplotype phasing in dairy cattle

ADD REPLYlink written 6 weeks ago by Kevin Blighe50k
gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe50k
Kevin Blighe50k wrote:

It's not exactly my research area (bovine studies); however, other researchers appear to have been able to impute the Bovine 50k microarray with other datasets, and Beagle seems to be used frequently across these and other studies:

The first study that I listed used, in addition to other studies, data from The Bovine Genome Database for the purposes of a reference panel for imputation.


ADD COMMENTlink written 6 weeks ago by Kevin Blighe50k
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