Picard
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.
Documentation
Usage on Bridges-2
To see what versions of Picard are available and if there is more than one, which is the default, along with some help, type
module spider picard
To use Picard, include a command like this in your batch script or interactive session to load the Picard module: (note ‘module load’ is case-sensitive):
module load picard
Usage on Bridges
To see what versions of Picard are available type
module avail picard
To see what other modules are needed, what commands are available and how to get additional help type
module help picard
To use Picard, include a command like this in your batch script or interactive session to load the Picard module:
module load picard
Be sure you also load any other modules needed, as listed by the module help picard command.