Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Free to use and open source under MIT License.
Version on CSC's Servers - Puhti: 2.27.4
To load Picard, load biokit:
module load biokit
To get a summary of available tools:
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.
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.
picard16 SamToFASTQ I=input.bam FASTQ=output.fastq