B6 variant vcf file

Question

[second_exon]

Hello,

I am trying to find heterozygous variants in the B6 (https://www.jax.org/strain/000664) mouse genome, which is used for producing mouse reference assemblies. Despite being inbred mice, I expect some level of heterozygosity. Before I start mapping and calling variants, is there a place where I can download the vcf file that contains heterozygous variants? Thank you.

[GenoMax]

Check https://www.mousegenomes.org/. It should contain the VCF files.

[second_exon]

Thank you. I have already checked the page, but unfortunately, they do not currently have the VCF file available for the B6. They do have it available for other prominent strains.

Answer 1

[Jeremy]

Digging a little further into the link provided by GenoMax, I found this website:

EVA

This contains VCFs of SNPs and indels for 52 inbred mouse strains. I would be surprised if C57BL/6NJ isn't included.

[second_exon]

Edit: C57BL/6NJ is a different strain (https://www.jax.org/strain/005304). But I am looking for C57BL/6J a.k.a B6 (https://www.jax.org/strain/000664). B6 is not included in the dataset you have shared.

Original: Thanks. Yes, it's indeed included - https://www.ebi.ac.uk/ena/browser/view/SAMEA1094237

[Kevin Blighe]

echo off