RefGraph Workflows Hackathon
This pipeline is for the use and testing of graph based methods for variant calling.
The aim is to allow the user to choose the reference graph construction method and the alignment / variant calling methods separately.
We also provide tools for reporting the results of the variant calling, that take advantage of the additional contextual information that using reference graphs provides.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The aim of this project is to separate the different parts of the variant calling process to allow the development of task specific tools. This is more in line with traditional variant calling where specific alignment tools may preform better for different organisms, but should not require a different downstream analysis for each output.
The h3abionet/h3arefgraph pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
h3abionet/h3arefgraph was originally written by the H3ABioNet RefGraph Team.