Question

Imputation and haplotype phasing in Bovine 50K SNP data

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4.6 years ago

kas • 0

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.

software error SNP ChIP-Seq • 1.4k views

ADD COMMENT • link 4.6 years ago by kas • 0

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

ADD REPLY • link 4.6 years ago by Kevin Blighe 87k

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

ADD REPLY • link 4.6 years ago by kas • 0

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

ADD REPLY • link 4.6 years ago by Kevin Blighe 87k

score 1 · Accepted Answer · 2019-09-07

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 feasibility of using low-density marker panels for genotype imputation and genomic prediction of crossbred dairy cattle of East Africa (take a look at the section entitled 'Genotypes')
Short communication: Imputation performances of 3 low-density marker panels in beef and dairy cattle

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.

Kevin