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Picard Tools

A few different versions of Picard Tools is available on all the PMACS HPC cluster nodes

[asrini@node107 ~]$ module show picard-1.96

module-whatis	 Picard Tools 
prepend-path	 CLASSPATH /opt/software/picard/picard-tools-1.96 
prepend-path	 PATH /opt/software/picard/picard-tools-1.96/bin 

[asrini@node107 ~]$ module show picard-tools-1.141 

module-whatis	 Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. 
prepend-path	 PATH /opt/software/picard-tools/1.141/bin 
prepend-path	 PICARD_JAR /opt/software/picard-tools/1.141/bin/picard.jar 

To use a version of Picard, load the appropriate module. For example, for Picard Tools: 1.141

[asrini@node107 ~]$ module load picard-tools-1.141

[asrini@node107 ~]$ module list
Currently Loaded Modulefiles:
  1) picard-tools-1.141

When loaded, this module will create an environment variable called $PICARD_JAR. To use this environment variable:

[asrini@node107 ~]$ java -jar $PICARD_JAR SortSam I=input.bam O=sorted.bam SORT_ORDER=coordinate

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