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.
Local Cromwell implementation of GATK4 germline variant calling pipeline
See the GATK website for more information on this toolset
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 /data volume storage partition.
Starting from short-read Illumina paired-end fastq