Picard

Java-Based HTS Data Manipulation Tools

Homepage Version(s): 3.1.1

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Picard requires an environment module

In order to use Picard, you must first load the appropriate environment module:

module load java/17 picard

A set of Java-based command line tools for working with high-throughput genomic sequencing (HTS) data.

Using Picard on the HPC

Connect to the HPC and run the following commands to create a folder and download a set of example files into it:

## Load the Required modules
$ ml java/17 picard

mkdir Picard_Test
$ cd Picard_Test
$ wget https://raw.githubusercontent.com/broadinstitute/picard/master/testdata/picard/illumina/mark_illumina_adapters_test.sam

## Run the Illumina Adapter Marking tool
$ java -jar ${PICARD_JAR} MarkIlluminaAdapters -I mark_illumina_adapters_test.sam -M metrics.out

For additional documentation, refer to the Picard Tool Reference.