Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

DNA-Seq pipeline

Here we provide the tools to perform paired end or single read DNA-Seq analysis including raw data quality control, read mapping, variant calling and variant filtering.

Pipeline Workflow

All analysis steps are illustrated in the pipeline ...