Mouse (MM10) SNPs

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jkozubek

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Join Date: Mar 2011

Posts: 18
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#1

Mouse (MM10) SNPs

09-28-2012, 09:35 AM

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
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vivek_

PhD Student

Join Date: Jul 2012

Posts: 164
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#2

09-28-2012, 11:35 AM

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.
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Elsie

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Join Date: Mar 2011

Posts: 85
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#3

03-27-2013, 05:26 PM

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