# picard-tools

## Summary

+ **Module Name:** picard-tools
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://broadinstitute.github.io/picard/](https://broadinstitute.github.io/picard/)

## Software Description

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.
## General Linux

The Picard command-line tools are packaged as executable jar files. For
a list of the available tools, please use the following command:

     module load picard-tools
     $PTOOL/picard.jar

OR: java -jar \$PICARD_DIR/picard.jar Picard commands can be invoked as
follows:

    java jvm-args -jar $PICARD_DIR/picard.jar PicardCommandName OPTION1=value1 OPTION2=value2...

where \"jvm-args\" is where you would insert specific Java JVM
arguments, if you would like to adjust those. For example, to run the
Picard insert size metrics tool, use this command:

    java -Xmx2g -jar $PICARD_DIR/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.