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Picard (tools)
Overview
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Version 2.18.7 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing Picard on the CSF. The software is released under the MIT license and all usage should adhere to that license.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/picard/2.18.7
Running the application
Please do not run Picard tools on the login node. Jobs should be submitted to the compute nodes via batch.
You may run the following command on the login node to see a list of tools provided by Picard:
picard -h
To see the help text specific to a particular tool, run:
picard toolname -h
For example:
picard CheckIlluminaDirectory -h
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings picard toolname args... # # Name of picard tool to run
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Given an example parallel jobscript, including suitable PE
Further info
Updates
None.