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

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 avail 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 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

Service: 
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