Friday, 16 November 2012

[galaxy-user] SNPeff on human genome

If you had tried to use SNPEff with your VCF for human genome on Galaxy you might have hit a snag when selecting for the correct genome. 

here's the explanation of how you should use SNPEff  
---------- Forwarded message ----------
From: Jennifer Jackson


SNPEff is available for use with the human reference genome in the GATK pipeline (the 1000 genomes version, called "Homo sapiens b37 (hg_g1k_v37)" in Galaxy). See the tool "NGS: GATK Tools (beta) -> Variant Annotator" and look in the list of "Annotations to apply".

The best documentation is at the GATK web site itself - we do not have extra tutorials available at this time (tools are still technically in 'beta'). Following the links on the tool forms for help are a start, but with the updated documentation structure they point to, it can be confusing. So, I pulled out the a relevant link that I think would be a good place to start, to learn more about this function (I just used the search function on the tool name, you could do same to explore other related info). You can also search for information about the genome source (obtained from GATK bundle last May).

Please note that the version of the genome you use very much matters with these tools - hg19 and hg_g1k_v37 are the same genome release, but differ in small ways when it comes to chromosome naming and some other organization (if using hg19 "full"). This can make it a tedious challenge to lift data between the two - we won't be able to help except with general guidelines - and the tools will not function if incorrect.

SO - the absolute top advice I can give you is to pick a genome and stick with it throughout your entire analysis to avoid issues. If you plan to use GATK for variant analysis, use hg_g1k_v37. (If you were using RNA-seq tools for expression analysis, I would recommend hg19, to take advantage of the iGenomes datasets).

Best wishes for your project,

Galaxy team

On 11/15/12 2:57 AM, David Sims wrote:

Is it possible to use SNPeff with genomes other than worm. This seems to be the only option on the main Galaxy server.


The Galaxy User list should be used for the discussion of  Galaxy analysis and other features on the public server  at  Please keep all replies on the list by  using "reply all" in your mail client.  For discussion of  local Galaxy instances and the Galaxy source code, please  use the Galaxy Development list:    To manage your subscriptions to this and other Galaxy lists,  please use the interface at:


  1. This doesn't seem to address the problem that the only option in the Galaxy SNPeff genome dropdown menu is C. elegans

  2. yes it does. it's a workaround to 'Adding SnpEff Annotations using VariantAnnotator' as per the link


Datanami, Woe be me