Question: SnpEff Error linked to inputs chromosome mismatches
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gravatar for federico.bernuzzi
15 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 wrote:

Dear all,

I have runned SnpEff, it seems to have worked and whilst looking through the results for a lot of the readings I get the following output, which I presume its not correct?

EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)

Any advice on what the error implies?

Many thanks

ADD COMMENTlink modified 15 months ago • written 15 months ago by federico.bernuzzi20
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There is probably a genome mismatch problem with the inputs.

Please review here for troubleshooting help to diagnose and correct: https://galaxyproject.org/support/chrom-identifiers/

If you cannot determine the proper method in the help above, or the fix does not resolve the problem, a bug report can be sent in if working at http://usegalaxy.org or the error can be reproduced there.

How-to report an error at Galaxy Main http://usegalaxy.org for review: Click on the green "bug" icon for the error dataset, leave all inputs, outputs, and troubleshooting datasets undeleted, plus please include in the comments a link to this Biostars post so we can associate the two.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
0
gravatar for federico.bernuzzi
15 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 wrote:

Hi Jen,

Many thanks for the reply. Yes you are correct that the problem is a mismatch. I went to the SnpEff documentation page and what the error means is that the input VCF file has chromosome names that do not match SnpEff's database and don't match reference genome either, since SnpEff's database are created using reference genome chromosome names.

I shall look into the problem.

Kind regards

FB

ADD COMMENTlink written 15 months ago by federico.bernuzzi20
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