ILRI Research Computing

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====== SnpEff ======
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a toolbox that allows you to filter and manipulate annotated files.

===== Information =====

  * Version: 5.1
  * Added: July, 2015
  * Updated: June, 2023
  * Link: https://pcingola.github.io/SnpEff/

===== Usage =====

See which versions of are available:
<code>$ module avail snpeff</code>

Load one into your environment and run it:
<code>$ module load snpeff/5.1
$ snpeff</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
$ sudo mkdir -p /export/apps/snpeff/5.1
$ sudo cp -r snpEff/* /export/apps/snpeff/5.1</code>