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Created At
Updated At
Workflow type
Workflow Description Language2
Submitter
Sarah Beecroft2
Space
Australian BioCommons2
Topic annotations
Genetic variation2
Whole genome sequencing3
Exome sequencing2
Bioinformatics1
DNA mutation1
Genomics1
Structural genomics1
More...
Operation annotations
Genetic variation2
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 ...
