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 pitzer
2.3.0 X* X*  
2.18.17     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.

Publisher/Vendor/Repository and License Type

The Broad Institute, Open source

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}.

Usage on Pitzer

Set-up

To configure your environment for use of Picard, run the following command: module load picard. The default version will be loaded. 

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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