B6 variant vcf file
1
0
Entering edit mode
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
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
echo off
ADD REPLY

Login before adding your answer.

Traffic: 1574 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