Pawsey Supercomputing Research Centre
OverviewSpace: Australian BioCommons
SEEK ID: https://workflowhub.eu/projects/42
Public web page: https://pawsey.org.au/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 24th Jun 2021
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https://orcid.org/0000-0002-3935-2279
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline
See the GATK website for more information on this toolset
Assumptions
- Using hg38 human reference genome build
- Running using HPC/SLURM scheduling. This repo was specifically tested on Pawsey Zeus machine, primarily running in the
/scratchpartition. - Starting from short-read Illumina paired-end fastq files as input
Dependencies
The following versions have been ...
DownloadLocal Cromwell implementation of GATK4 germline variant calling pipeline
See the GATK website for more information on this toolset
Assumptions
- Using hg38 human reference genome build
- Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the
/datavolume storage partition. - Starting from short-read Illumina paired-end fastq ...
