Question: How can I use SNPeff with this genome?
0
gravatar for madkitty
4.4 years ago by
madkitty570
Canada
madkitty570 wrote:

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? 

 

 

snp effect snpeff • 3.1k views
ADD COMMENTlink modified 4.4 years ago by Charles Warden5.8k • written 4.4 years ago by madkitty570
0
gravatar for Charles Warden
4.4 years ago by
Charles Warden5.8k
Duarte, CA
Charles Warden5.8k wrote:

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

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

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.

ADD COMMENTlink written 4.4 years ago by Charles Warden5.8k

Well thanks a lot but .. it's waaaaaaaay to 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? 

ADD REPLYlink written 4.4 years ago by madkitty570

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:

https://usegalaxy.org/

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

ADD REPLYlink written 4.4 years ago by Charles Warden5.8k
Thanks, I've checked Galaxy and they only offer one c elegans reference genome .. Thank you for your help anyway.
ADD REPLYlink written 4.4 years ago by madkitty570
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