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Question: Snpeff
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gravatar for Andréanne Morin
5.3 years ago by
Andréanne Morin • 10
Andréanne Morin • 10 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
snpeff snp • 1.3k views
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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by Andréanne Morin • 10
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gravatar for Jennifer Hillman Jackson
5.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k
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