Difference between revisions of "Picard"
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== Introduction == | == Introduction == | ||
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 [http://samtools.github.io/hts-specs/SAMv1.pdf SAM specification] and the [http://samtools.github.io/hts-specs/VCFv4.3.pdf VCF specification]. | 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 [http://samtools.github.io/hts-specs/SAMv1.pdf SAM specification] (PDF) and the [http://samtools.github.io/hts-specs/VCFv4.3.pdf VCF specification] (PDF). | ||
== Installed version == | == Installed version == | ||
The currently installed version of Picard on the cluster is '''2.9.0'''. | |||
== Using Picard on the HPC cluster == | == Using Picard on the HPC cluster == | ||
If you want to use Picard on the HPC cluster, you have to load the corresponding module first. To do so, use the command | |||
module load picard | |||
Since there is only one version of picard installed at the moment, specifying a version is not necessary. If there would be another version installed, specifying the version would look like this: | |||
module load picard/2.9.0 | |||
After loading the module, you will see this message: | |||
To execute picard run: java -jar $EBROOTPICARD/libs/picard.jar | |||
It tells you how to run picard. | |||
== Documentation == | == Documentation == | ||
More informations can be found on the [https://broadinstitute.github.io official homepage]. If you are looking for a command line overview, you can should look [https://broadinstitute.github.io/picard/command-line-overview.html here]. | |||
Latest revision as of 13:58, 30 March 2017
Introduction
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 (PDF) and the VCF specification (PDF).
Installed version
The currently installed version of Picard on the cluster is 2.9.0.
Using Picard on the HPC cluster
If you want to use Picard on the HPC cluster, you have to load the corresponding module first. To do so, use the command
module load picard
Since there is only one version of picard installed at the moment, specifying a version is not necessary. If there would be another version installed, specifying the version would look like this:
module load picard/2.9.0
After loading the module, you will see this message:
To execute picard run: java -jar $EBROOTPICARD/libs/picard.jar
It tells you how to run picard.
Documentation
More informations can be found on the official homepage. If you are looking for a command line overview, you can should look here.
