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