Mouse (MM10) SNPs

[jkozubek]

Hello,

Does anyone know if there is a VCF file of SNPs and Indels available yet for MM10 (mouse), and where to obtain it?

I need this for GATK.

Jim

[vivek_]

I don't think there's a dbSNP VCF for mm10 yet.

You'll likely have to download the snp128.txt from the UCSC annotation database for mm9, convert it to VCF and lift over to mm10 coordinates. Its a little taxing but that's the only workflow I'm aware of.

[Elsie]

See ftp://ftp.ncbi.nih.gov/snp/organisms...00--README.txt