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
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, installation instructions and tutorials can be found at:
https://odelaneau.github.io/shapeit5/
This project is licensed under the MIT License - see the LICENSE file for details