Picard Tools

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

• Picard Tools
  • License
  • Available
  • Usage
  • Support
  • More information

License

Free to use and open source under MIT License.

Available

• Roihu-CPU: 3.3.0, via the bio-apps module.

Usage

Picard is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Picard module:

module load bio-apps/v202603
module load picard/3.3.0

To get a summary of available tools:

picard

Please note that in the Picard manual commands start with java -jar picard.jar. On Roihu it is easiest to run Picard through the picard wrapper, so substitute that with just picard.

Example:

picard SamToFastq I=input.bam FASTQ=output.fastq

If you need to specify Java options for Picard (for example to control the Java heap size), you can run the jar directly with java — the module sets the $PICARD environment variable to the Picard jar file.

Example:

java -Xmx16g -jar $PICARD SamToFastq I=input.bam FASTQ=output.fastq

Support

CSC Service Desk

More information

• Picard home page
• Detailed tool documentation

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