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picard-software

Picard tools

A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.

Information

Usage

See versions of picard which are available:

$ module avail picard

Run picard:

$ java -jar /export/apps/picard/2.25.5/picard.jar

Note: Picard tools are CPU hungry; please use a minimum of 6 CPUs in your batch job when running tools from this suite.

Note: Picard makes use of temporary storage in /tmp during analysis by default. You will probably run into "No space left on device" errors unless you specify a different temp directory, for example: TMP_DIR=/var/scratch.

Installation

Notes from the sysadmin during installation:

$ wget https://github.com/broadinstitute/picard/releases/download/2.25.5/picard.jar
$ sudo mkdir -p /export/apps/picard/2.25.5
$ sudo cp picard.jar /export/apps/picard/2.25.5
picard-software.txt · Last modified: 2021/05/20 17:30 by aorth