PanGenie

A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph. Genotypes are computed based on read k-mer counts and a panel of known, fully assembled haplotypes. A description of the method can be found here: https://doi.org/10.1038/s41588-022-01043-w

For detailed documentation, please visit the PanGenie Homepage.