Picard-tools

Description

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page. Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Home Page

http://picard.sourceforge.net

Documentation

https://broadinstitute.github.io/picard/

License

Unknown

Usage

Use

module avail picard-tools

to see which versions of picard-tools are available. Use

module load picard-tools

or

module load picard-tools/version

to get access to picard-tools. To run picard-tools in a job script, use

java -jar $PICARD_ROOT/picard.jar options ...

OR

java -jar $PICARD_JAR options ...