Question: Bundle file for mouse
0
gravatar for ARich
2.6 years ago by
ARich90
United States
ARich90 wrote:

Hi All,

I am currently struggling with Bundle file for mouse genome (mm10) I searched and found this: http://hgdownload.soe.ucsc.edu/downloads.html#mouse However i am not sure how to use this information and translate it into VCF for GATK? Any kind of suggestion would be of great help!

Thanks!

snp next-gen • 1.4k views
ADD COMMENTlink modified 2.6 years ago by WouterDeCoster44k • written 2.6 years ago by ARich90
2

This workflow might be helpful as well: https://github.com/igordot/genomics/blob/master/workflows/gatk-mouse-mm10.md

ADD REPLYlink written 2.6 years ago by igor11k
1

A: Where To Download Mouse Mm10 Dbsnp Database With Vcf Format

ADD REPLYlink written 2.6 years ago by said342790

If you are referring to a bundle file for sequence/annotation/aligner indexes then take a look at iGenomes page. This would be needed to align your reads and then eventually get a VCF file.

ADD REPLYlink written 2.6 years ago by genomax91k

Have you read this on GATK ?

ADD REPLYlink written 2.6 years ago by Nandini880
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