Hello Andréanne,

If you plan to use the data with GATK, then VCF format would be best, although other input file options are permitted. Fit the format to one of the datatypes, then assign that datatype to have it recognized by the tool (click on the pencil icon to do this), then run the SNPEff tool. An example of a properly formatted txt/tabular file is in the example data in the full instructions at the bottom of the SNPEff tool form:
http://snpeff.sourceforge.net/SnpEff.html

Best,

Jen
Galaxy team

On 7/29/13 7:58 AM, Andréanne Morin wrote:

Hello,

I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format :

Chr location ref allele alt allele

1 1234567 A T/C

What am I doing wrong?

Thanks,

Andréanne
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