Picard

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Availability and Restrictions

Versions

The following versions of Picard are available on OSC clusters:

Version Oakley Owens
2.3.0 X* X*
* Current default version

You can use  module spider picard to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Picard is available to all OSC users without restriction.

Usage

Usage on Oakley

Set-up

To configure your environment for use of Picard, run the following command: module load picard. The default version will be loaded. To select a particular Picard version, use module load picard/version. For example, use  module load picard/2.3.0. to load Picard 2.3.0.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load picard, a new environment variable, PICARD, will be set. Thus, users can use the software by running the following command: java -jar $PICARD {other options}.

Usage on Owens

Set-up

To configure your environment for use of Picard, run the following command: module load picard. The default version will be loaded. To select a particular Picard version, use module load picard/version. For example, use module load picard/2.3.0. to load Picard 2.3.0.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load picard, a new environment variable, PICARD, will be set. Thus, users can use the software by running the following command:  java -jar $PICARD {other options}.

Further Reading

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