A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.

• Version: 2.8.2
• Added: March, 2015
• Updated: February, 2017
• Link: https://broadinstitute.github.io/picard

See versions of picard which are available:

$ module avail picard

Load and run picard:

$ module load picard/2.8.2
$ picard

Note: Picard tools are CPU hungry; please use a minimum of 6 CPUs in your batch job when running tools from this suite.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/broadinstitute/picard/releases/download/2.8.2/picard-2.8.2.jar
$ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/

I created a generic picard wrapper for picard tools, as it must otherwise be run with java -jar .. and is rather user-unfriendly.

/export/apps/picard/2.8.2/picard:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/picard.jar $*