Picard

module avail picard/

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Usage

Be aware that Picard needs a defined `$SCRATCHDIR` variable for successful running.

To run Picard version <= 2.22.1  you need Java as well - load manually `module add jdk/`.

Users can list available tools:

java -jar $PICARD

And run individual tools, for example:

java -jar $PICARD CreateSequenceDictionary -h #will print manual page
java -jar $PICARD CreateSequenceDictionary R=reference.fasta O=reference.dict

Since version 2.27.5, the usage is more straightforward.

module add picard # it will load the newest version of Picard
picard <program name> -h

Java processes within Picard may exceed the quota for saving temporary files in the root directory (/tmp). When calculation fails with something like Caused by: java.io.IOException: Disk quota exceeded, call the command

export JAVA_TOOL_OPTIONS="-Djava.io.tmpdir=$SCRATCHDIR"

before starting Picard. This command redirects temporary files to the scratch.