Picard

Introduction

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification (PDF) and the VCF specification (PDF).

Installed version

The currently installed version of Picard on the cluster is 2.9.0.

Using Picard on the HPC cluster

If you want to use Picard on the HPC cluster, you have to load the correspondig module first. To do so, use the command

module load picard

Since there is only one version of picard installed at the moment, specifying a version is not necessary.

After loading the module, you will see this message:

To execute picard run: java -jar $EBROOTPICARD/libs/picard.jar

It tells you how to run picard.

Documentation

More informations can be found on the official homepage. If you are looking for a command line overview, you can should look here.