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Created At
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Workflow type
Workflow Description Language2
Submitter
Sarah Beecroft2
Anna Syme16
Tracy Chew9
Johan Gustafsson4
Mike Thang3
Georgina Samaha2
Marco De La Pierre1
Valentine Murigneux1
Richard Lupat1
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Space
Australian BioCommons2
Maturity
Work-in-progress2
Work-in-progress
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 ...
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Work-in-progress
Local 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 ...
