Picard

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Description

picard website  

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.

Execution Environment and 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.

How To Run

There is a convenience symlink to the latest picard directory in the addition to the $HPC_PICARD_DIR set by the picard module as

/apps/picard/bin

So picard jars can be run both as

java -Xms1g -Xmx8g -jar /apps/picard/bin/ReorderSam.jar

and

java -Xms1g -Xmx8g -jar $HPC_PICARD_DIR/ReorderSam.jar

To run picard tools with non-default java memory settings you can set the minimum and the maximum heap memory in the command. For example:

java -Xms1g -Xmx8g -jar /apps/picard/bin/ReorderSam.jar INPUT=input.bam OUTPUT=output.bam VALIDATION_STRINGENCY=LENIENT REFERENCE=ref.fasta CREATE_INDEX=true