Picard

module avail picard/

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Usage

Warning

Be aware that Picard needs defined SCRATCHDIR variable for successful running.

Warning

To run Picard version <= 2.22.1 you need Java as well - load manually module add jdk/.

Users can list available tools:

java -jar $PICARD

And run individual tools, for example:

java -jar $PICARD CreateSequenceDictionary -h #will print manual page
java -jar $PICARD CreateSequenceDictionary R=reference.fasta O=reference.dict

Since version 2.27.5, the usage is more straightforward.

module add picard # it will load the newest version of Picard
picard <program name> -h