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.
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.