Question: Snpeff
gravatar for Andréanne Morin
5.3 years ago by
Andréanne Morin10 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
ADD COMMENTlink modified 5.3 years ago by Jennifer Hillman Jackson25k • written 5.3 years ago by Andréanne Morin10
gravatar for Jennifer Hillman Jackson
5.3 years ago by
United States
Jennifer Hillman Jackson25k 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: Best, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.3 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour