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Intro

Welcome to the vcfdist wiki! This wiki is intended to document vcfdist for both users and developers.

If you have any questions, ideas, or feedback: please open a new discussion.

If you found a bug or have a feature request: please submit an issue.

For information on vcfdist updates: check the latest releases.

Citing vcfdist

If you use vcfdist in your research, please cite the following works:

[Nature Comms] vcfdist: Accurately benchmarking phased small variant calls in human genomes

@article{dunn2023vcfdist,
  author={Dunn, Tim and Narayanasamy, Satish},
  title={vcfdist: Accurately benchmarking phased small variant calls in human genomes},
  journal={Nature Communications},
  year={2023},
  volume={14},
  number={1},
  pages={8149},
  issn={2041-1723},
  doi={10.1038/s41467-023-43876-x},
  URL={https://doi.org/10.1038/s41467-023-43876-x}
}

[bioRxiv] Jointly benchmarking small and structural variant calls with vcfdist

@article{dunn2024vcfdist,
  author={Dunn, Tim and Zook, Justin M and Holt, James M and Narayanasamy, Satish},
  title={Jointly benchmarking small and structural variant calls with vcfdist},
  journal={bioRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2024.01.23.575922},
  URL={https://doi.org/10.1101/2024.01.23.575922}
}

Index

• Home
• Overview
• Input Parameters
• Clustering
• Variant Normalization / Realignment
• Precision & Recall Calculation
• Phasing Analysis
• Outputs
• Citations