Bundle file for mouse

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6.8 years ago

ARich ▴ 130

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 • 3.0k views

ADD COMMENT • link updated 6.8 years ago by WouterDeCoster 47k • written 6.8 years ago by ARich ▴ 130

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

ADD REPLY • link 6.8 years ago by igor 13k

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

ADD REPLY • link 6.8 years ago by said3427 ▴ 120

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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.