Picard is a collection of 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 SAMtools software package provides similar functionality.
The Picard command-line tools are packaged as executable jar files. They can be invoked as follows:
module load picard-tools java jvm-args -jar $CLASSPATH/picard.jar PicardCommandName OPTION1=value1 OPTION2=value2...
For example, to run the insert size metrics tool, use this command:
java -Xmx2g -jar $CLASSPATH/picard.jar CollectInsertSizeMetrics INPUT=alignment.bam OUTPUT=insertmetrics.txt HISTOGRAM_FILE=histogram.png
Most of the commands are designed to run in 2GB of JVM, so the JVM argument -Xmx2g is recommended. Some picard tools require R, in which case you need to load the R module:
module load R
See https://broadinstitute.github.io/picard/command-line-overview.html for information about individual tools and options.