B6 variant vcf file
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15 months ago
second_exon ▴ 210

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.

Mouse B6 vcf • 1.1k views
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Check https://www.mousegenomes.org/. It should contain the VCF files.

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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.

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15 months ago
Jeremy ▴ 930

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.

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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

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