VectorHAP

A Nextflow pipeline for phasing SNP genotypes for a cohort of multiple samples

VectorHAP was built and tested on Nextflow version 22.04, and Singularity version 3.6.4. Assuming you already have Nextflow, and Singularity, clone the repository:
git clone https://github.com/eddUG/VectorHap.git

If Singularity is not available, the pipeline assumes all dependencies with the correct versions are available in the execution environment.
You can run the pipeline as follows:

nextflow /path/to/repository/main.nf \
        -c /path/to/repository/nextflow.config \ 
        -profile standard \
        -with-trace \
        -resume \
        --project_id XXXXXXXXXX \
        --input_manifest /path/to/input_manifest.tsv

Authors and Acknowledgements

This pipeline has been implemented as part of my vector genomics fellowship rotation to the Data Analysis and Engineering Team at the Wellcome Sanger Institute's Genomic Surveillance Unit. The methodology implemented by early versions of the pipeline is described by Alistair et. al.

The methods and approach continue to be actively developed by the GSU.