Picard
Description
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
License
Apache v 2.0, MIT licence.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of picard and load default version of picard as
module avail picard/ # list available modules module load picard # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail picard
and choose explicit version you want to use. Be aware that Picard needs defined Scratch storage for successful running.
Initialization makes available also module java 1.8.0_60 and system variable $PICARD pointing into Picard Tools install dir /software/picard/2.9.0/build/libs/picard.jar.
Users can list available tools:
java -jar $PICARD281
And run individual tools, for example:
java -jar $PICARD281 CreateSequenceDictionary -h #will print manual page java -jar $PICARD281 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
Documentation
Dokumentation is available at https://broadinstitute.github.io/picard/command-line-overview.html#Overview, FAQ can be found on wiki of Picard Tools project on SourceForge.