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 | Owens | Pitzer | Cardinal |
|---|---|---|---|
| 2.3.0 | X* | ||
| 2.18.17 | X* | ||
| 3.0.0 | X |
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. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
The Broad Institute, Open source
Usage
Usage on Owens
Set-up
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
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}.
