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).
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
The workflow sample "Variation Annotation with SnpEff" can be found in the "NGS" section of the Workflow Designer samples.
The opened workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff.png"/> <br> </center> |
The wizard has 3 pages.
Input Variations: On this page you must input variations file(s).
<center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_1.png"/> <br> </center> |
<center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_2.png"/> <br> </center> |
<center> <br> <img src="/wiki/download/attachments/16121886/Variation Annotation with SnpEff_3.png"/> <br> </center> |