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.

The instruction webpage mentioned most of the commands are designed to run in 2GB of JVM, so the JVM argument -Xmx2g is recommended. However, we do notice some job require more than 2g otherwise the job will finish with wrong output files without errors (users won't know the output is incomplete).

Sample Session on Helix

Picard *.jar files are located under:

/usr/local/picard

To run picard on 20g of memory, on helix, type:

$ java -Xmx20g -jar /usr/local/picard/*.jar

User can change the number '20' according to memory requirement of the job.

Documentation

http://picard.sourceforge.net/command-line-overview.shtml#Overview