Paper version

The paper is out, check it out on https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011092

@article{wertenbroek2024improving,
  title={Improving population scale statistical phasing with whole-genome sequencing data},
  author={Wertenbroek, Rick and Hofmeister, Robin J and Xenarios, Ioannis and Thoma, Yann and Delaneau, Olivier},
  journal={PLoS genetics},
  volume={20},
  number={7},
  pages={e1011092},
  year={2024},
  publisher={Public Library of Science San Francisco, CA USA}
}

With this we are pleased to release the first version of SAPPHIRE !

Updates, improvements, and fixes will likely come so please clone the main branch on https://github.com/rwk-unil/sapphire if you want to run the latest version.

Preprint pre-release

This tag is the preprint pre-release of the code. It has been used to rephase the 200k release of the UK Biobank.

Link to BioRxiv preprint : https://www.biorxiv.org/content/10.1101/2023.12.07.570528v1

Please use the main branch on https://github.com/rwk-unil/pp as the code is still evolving.

Ultralight Rare Variant Phase Caller

Ultralight Rare Variant Phase Caller

Binary files

• hts-ref.zip contains human reference files needed for reading CRAM files without downloading them from https://www.ebi.ac.uk