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Segmented HAPlotype Estimation and Imputation Tools version 5 (SHAPEIT5)

SHAPEIT5 estimates haplotypes in large datasets, with a special focus on rare variants.

  • docker: all script needed to build a docker file comprising all binaries
  • docs: documentation in html
  • ligate: ligate multiple phased BCF/VCF files into a chromosome length file
  • maps: genetics maps in b37 and b38
  • phase_common: phase common sites, typically SNP array data
  • phase_rare: phase rare variants onto a scaffold of common variants
  • static_bins: static binaries of all executables
  • switch: compute switch error rate and genotyping error rate given simulated or trio data
  • tasks: scripts used to phase large datasets, good base to start pipelining
  • test: simulated data for first-step testing of the method
  • versions: versioning

Citation

If you use SHAPEIT5 in your research work, please cite the following paper:

Hofmeister RJ, Ribeiro DM, Rubinacci S., Delaneau O. Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. BiorXiv (2022)

Documentation

Documentation, installation instructions and tutorials can be found at:

https://odelaneau.github.io/shapeit5/

License

This project is licensed under the MIT License - see the LICENSE file for details

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  • C++ 83.7%
  • Shell 14.3%
  • Makefile 1.6%
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