Differences

This shows you the differences between two versions of the page.

--- snpeff-software [2015/07/28 07:13] – created aorth
+++ snpeff-software [2023/06/12 17:49] (current) – [Usage] aorth
@@ Line 1: / Line 1: @@
 ====== 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: 4.1g
+  * Version: 5.1
   * Added: July, 2015
-  * Link: http://snpeff.sourceforge.net/SnpEff.html
+  * Updated: June, 2023
+  * Link: https://pcingola.github.io/SnpEff/
 ===== Usage =====
-See versions of snpeff which are available:
+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 ======
@@ Line 17: / Line 24: @@
 <code>$ cd /tmp
-$ wget 'http://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip?r=&ts=1438066881&use_mirror=liquidtelecom' -O snpEff_latest_core.zip
+$ wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
-$ unzip snpEff_latest_core.zip
+$ sudo mkdir -p /export/apps/snpeff/5.1
-$ sudo mkdir -p /export/apps/snpeff/4.1g
+$ sudo cp -r snpEff/* /export/apps/snpeff/5.1</code>
-$ sudo cp -r snpEff/* /export/apps/snpeff/4.1g</code>
-Create shell script wrappers for ''snpEff.jar'' and ''SnpSift.jar'', ie:
-<code>#!/bin/env bash
-TOP=$(dirname $0)
-# examples/examples.sh uses 4g heap
-java -Xmx4g -jar $TOP/snpEff.jar $*</code>