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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.

Picard does not have its own mailing lists. Please use the SAMTools mailing Lists for Picard-related correspondence. Template:App Location

Available versions

  • 1.54

Running the application using modules

To use picard with the environment modules system at HPC the following commands are available:

Get module information for picard:

$module spider picard

Load the default application module:

$module load picard

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_PICARD_DIR - directory where picard is located.

See the samtools HPC wiki page for more details on Samtools.