Downloading mm10 reference from

Hi all,

Is it possible to download the exact mm10 reference file used by galaxy directly into my computer? I’m trying to run a variant caller called MuTect and the error I am getting is that the mm10 file I am supplying and my aligned files (which i aligned on galaxy using BowTie and the built-in mm10 database) do not have the same order of contigs (ERROR MESSAGE: Input files reads and reference have incompatible contigs: Order of contigs differences, which is unsafe). I figured out that a few chromosomes are out of order, which means the mm10 on my computer isn’t exactly the same as the mm10 used by galaxy. So the easiest way to fix this error message is to get the exact mm10 file used by galaxy and supply it to MuTect instead of re-aligning everything to the current mm10 file I have on my computer.


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Reference file for what tool? E.g. hisat2 is here:

You can browse others at and

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Thanks for your reply. I didn’t realize there were different reference files for difference tools. I aligned using BowTie so I downloaded mm10 from that folder. Is there a link to the index (.fai) file?

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Explore all of the data/indexes available for mm10 in the second link @marten set.

/seq has the .fa. (fasta)
/samtools has a link to that same .fa plus the sam index .fai.

You’ll probably want to get them all and then set up your .loc files to match.

Downloading and using pre-built indexes is the more different way to install a genome. Using Data Managers is much better if you prefer to use the administrator web interface. To have the genomes match up, just get the fasta, then use that “from the history” when running other DMs, including Samtools.

More help is in this prior Q&A: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Thank you for your reply. I’ve located these files and MuTect seems to be running!

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Super, glad you sorted this out!