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B6 variant vcf file

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
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updated by Kevin Blighe Kevin Blighe • written by second_exon 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.

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written by second_exon second_exon

1 answer

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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written by Jeremy • Jeremy

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