SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
A typical SnpEff use case would be:
-Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
-Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
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If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
Workflow Sample Location
The workflow sample "Variation Annotation with SnpEff" can be found in the "NGS" section of the Workflow Designer samples.
Workflow Image
The opened workflow looks as follows:
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<center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff.png"/> <br> </center> |
Workflow Wizard
The wizard has 3 pages.
Input Variations: On this page you must input variations file(s).
HTML <center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_1.png"/> <br> </center>
- SnpEff Parameters: On this page you can modify SnpEff parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_2.png"/> <br> </center>
- Output: On this page you need input output parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_3.png"/> <br> </center>