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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

License

Free to use and open source under MIT License.

Available

  • Roihu: 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

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