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Warning!

Puhti and Mahti will be decommissioned after Roihu becomes available. Users should clean up unnecessary files and move any required data by the end of August 2026. See the Roihu data preparation instructions for details.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

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

  • Puhti: 2.27.4, 2.27.5, 3.0.1, 3.1.1

Usage

To load Picard, load module: 

module load picard

Note: The biokit module comes with Picard version 2.27.5 due to Java version compatibility with other software. To use newer version of Picard, load the picard module.

To get a summary of available tools: 

picard

Please note that in the Picard manual commands start with "java -jar picard.jar". In Puhti it is easiest to run Picard through a wrapper script, so substitute that with just picard.

Example: 

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

By default picard can use up to 8 GB  of memory. If your analysis task requires more memory, you can launch picard with commands, picard16, picard32 and picard64 that reserve 16, 32 or 64 GB of memory respectively.

Example: 

picard16 SamToFASTQ I=input.bam FASTQ=output.fastq

If you need to specify Java options for Picard you can use java -jar $PICARD.

Example: 

java -Xmx128g -jar $PICARD  SamToFASTQ I=input.bam FASTQ=output.fastq

More information