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
  • More information

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

• Picard home page
• Detailed tool documentation

Do you find this page useful?

Yes

Thank you for your feedback!

No

Thank you! Your feedback is appreciated.

Please let us know how we could improve this page by contacting us or by creating an issue in GitHub. You can also edit this page yourself and contribute your improvements by creating a pull request.