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

• Version: 2.17.0
• Added: March, 2015
• Updated: December, 2017
• Link: https://broadinstitute.github.io/picard

See versions of picard which are available:

$ module avail picard

Load and run picard:

$ module load picard/2.17.0
$ picard

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

Note: Picard makes use of temporary storage in /tmp during analysis by default. You will probably run into "No space left on device" errors unless you specify a different temp directory, for example: TMP_DIR=/var/scratch.

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/picard/2.17.0
$ wget https://github.com/broadinstitute/picard/releases/download/2.17.0/picard.jar
$ sudo cp picard.jar /export/apps/picard/2.17.0

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/2.17.0/picard:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/picard.jar $*