Nextflow Pipeline for DeepVariant

This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.

Quickstart Guide

1. Edit the pipeline_params.yml file to include:

• samples: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to '' if not required), and the model type.
• ref: path to the reference FASTA (ensure ...

Somatic-ShortV @ NCI-Gadi is a variant calling pipeline that calls somatic short variants (SNPs and indels) from tumour and matched normal BAM files following GATK's Best Practice Workflow. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel. ...