Picard Tools

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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. 

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The Picard command-line tools are packaged as executable jar files. They can be invoked as follows:

java jvm-args -jar $CLASSPATH/PicardCommand.jar OPTION1=value1 OPTION2=value2...

For example, to run the insert size metrics tool, use this command:

java -Xmx2g -jar $CLASSPATH/CollectInsertSizeMetrics.jar INPUT=alignment.bam OUTPUT=insertmetrics.txt

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 http://picard.sourceforge.net/command-line-overview.shtml for information about individual tools and options.

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