Genotype File

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3 months ago

goyal.shiwali ▴ 20

Hello Can anyone please tell me from where I can download the genotype files in vcf format for C57BL/6J and FvBN mice. I need this genotype file for eQTL analysis

Thanks

Genotype • 512 views

ADD COMMENT • link updated 3 months ago by dsull ★ 6.9k • written 3 months ago by goyal.shiwali ▴ 20

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This data should be available in: https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/

Please take a look at the README.txt file for information.

ADD REPLY • link 3 months ago by GenoMax 147k

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Hello Thanks for sharing the link, but this does not have C57Bl/6J and FvBN. Instead they have C57BL6/NJ and FvBN/J.

ADD REPLY • link 3 months ago by goyal.shiwali ▴ 20

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C57Bl/6J is the mouse reference genome so therefore it won't have its own record in the VCF file. VCF files represent the variants with respect to the C57Bl/6J mouse.

ADD REPLY • link 3 months ago by dsull ★ 6.9k

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Will move my original answer to a comment since it does not include the strains you are looking for.

https://www.informatics.jax.org/snp has the strains and you can query SNP's by regions but I don't see a way to download entire VCF's easily. You can write to MGI helpdesk and ask if the files are available.

ADD REPLY • link 3 months ago by GenoMax 147k

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