Phasing and imputation with Shapeit
0
0
Entering edit mode
7 weeks ago
PeterKW ▴ 40

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.

imputation Shapeit phasing • 122 views
ADD COMMENT

Login before adding your answer.

Traffic: 2465 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6