Introduction

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.

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.

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

Source: http://picard.sourceforge.net/index.shtml http://sourceforge.net/projects/picard/

Modulefile Usage

module load bioinformatics/picard/1.68 
OR module load bioinformatics/picard/2.7.1

 module display bioinformatics/picard/1.68
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/sw/com/modulefiles/bioinformatics/picard/1.68:

module-whatis    adds picard directories to PATH etc.
prepend-path     CLASSPATH /sw/bioinformatics/picard-tools/1.68/jar
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Installation

mkdir /sw/bioinformatics/picard-tools/1.68/src
unzip picard-tools-1.68.zip

Reference