Phasing and imputation with Shapeit

Question

[PeterKW]

Hi,

I wish to do some imputation and phasing analysis using Shapeit. This is my first time. I have bovine data (1 - 29 chromosomes) in VCF format. I have reference population with 4k animals and 10k animals to be imputed for about 23k SNPs.

I have tried to follow the illustrations in the forum but I am struggling to get this done. Is there anyone with some bovine genetic map or an illustration of how I can create one and how to use my reference which I need to first phase and impute a few randomly missing calls. I would like some help on how to impute and phase with and without a reference.

Thanks.