How can I figure out where a mouse (C57BL/6J) genome is heterozygous?

Question

[kaush123]

Hi!

The mouse strain C57BL/6J is used as a reference genome in SNP variant call files created by the mouse genomes project for other in-bred mouse strains. However, I am interested in figuring out if C57BL/6J itself is heterozygous at those SNP locations. Is there a straight forward way of figuring that out?

[Ram]

how-to is not a relevant tag here - you're not writing a how-to tutorial, and "How can I do this" questions don't need the how-to tag.

Answer 1

[predeus]

If you are using a haploid reference generated from C57BL/6J, you would need to find a public WGS data from C57BL/6J, map it to your reference, and call variants. I am not sure if you're using the same reference that was reported here, but it seems like the data from this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553538/) deposited here (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA318985) would be a good place to start.

Answer 2

[bk11]

If you have PLINK binary files (bed/bim/fam), you could check heterozygosity at your SNPs locations using a simple command-

https://zzz.bwh.harvard.edu/plink/summary.shtml

plink --file data --test-mishap