How can I use SNPeff with this genome?

Question

[madkitty]

I use this mtDNA reference genome (Donkey): http://www.ncbi.nlm.nih.gov/nuccore/NC_001788.1

I have a list of SNPs from SAMtools that I need to annotate with that genome. I thought SNPeff could be a good alternative, but I don't see where I can upload my own reference genome in there. Any suggestions or alternative?

Answer 1

[Charles Warden]

SnpEff has pretty good documentation. Here are the instructions on how to create a custom database:

In practice, I've never had to do this. There are a large number of organisms with pre-defined databases:

http://snpeff.sourceforge.net/SnpEff_manual.html#intro

However, these are typically for whole genomes. In fact, I'm not sure how well it will work with only a mitochondrial genome sequence. Nevertheless, it won't hurt to give it a try.

[madkitty]

Well thanks a lot but .. it's waaaaaaaay too complicated for me. Don't we have a simple interface with a "upload your reference genome", and a "upload your list of SNPs" and done?

[Charles Warden]

I think most web-based annotation tools for designed with human genome annotation in mind. I've only run SnpEff locally, but there is an implementation on Galaxy.

I'm not sure if it is possible to analyze a non-standard reference in the main Galaxy server, but you can see if the SnpEff developer has any suggestions: http://snpeff.sourceforge.net/about.html#help

[madkitty]

Thanks, I've checked Galaxy and they only offer one c elegans reference genome .. Thank you for your help anyway.