This repository holds the source code and data files for the paper Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes", Bioinformatics 2019 (proceedings of ISMB/ECCB 2019).

Slides from the ISMB talk are available

The integrated phasing method uses the HapCUT2 and SHAPEIT2 tools to phase individual genomes (diploid) using sequence reads and population data. Please see pipeline.md on instructions on how to use the tool.