The Practical Haplotype Graph (PHG) is a graph-based computational framework that represents large-scale genetic variation and is optimized for plant breeding and genetics [@doi:10.1093/bioinformatics/btac410]. Using a pangenome approach, each PHG stores haplotypes (the sequence of part of an individual chromosome) to represent the collective genes of a species. This allows for a simplified approach for dealing with large scale variation in plant genomes. The PHG pipeline provides support for a range of genomic analyses and allows for the use of graph data to impute complete genomes from low density sequence or variant data.
Users can access the haplotype data either with direct calls to the PHG embedded server or indirectly using the rPHG library from an R environment. The PHG server accepts BrAPI queries to return information on sample lists and the variants used to define the graph's haplotypes. In addition, PHG users utilize the BrAPI variant sets endpoint query to return links to VCF files containing haplotype data. Work on the PHG is ongoing and it is expected to support additional BrAPI endpoints that allow for fine tuned slicing genotypic data in the near future.