picard-tools

Module Name

picard-tools

Last Updated On

11/28/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

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.

Default

2.25.6

Other Modules

1.126, 1.133, 1.140, 1.79, 1.83, 2.1.1, 2.18.16, 2.23.3, 2.25.6, 2.3.0, 2.9.0

Default

2.25.6

Other Modules

1.126, 1.133, 1.140, 1.79, 1.83, 2.1.1, 2.18.16, 2.23.3, 2.25.6, 2.3.0, 2.9.0

Default

2.25.6

Other Modules

1.126, 1.133, 1.140, 1.79, 1.83, 2.1.1, 2.18.16, 2.23.3, 2.25.6, 2.3.0, 2.9.0