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Picard Tools

Description

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

Version on CSC's Servers - Puhti: 2.27.4

Usage

To load Picard, load biokit: 

module load biokit

To get a summary of available tools: 

picard

Please note that in the Picard manual commands start with "java -jar picard.jar". In Puhti Picard needs to be run 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.

Example: 

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

Manual