The Great Genotyper

The Great Genotyper is an alignment-free population genotyper of small and structural variants. It begins by preprocessing raw sequencing data to create a Counting Colored De Bruijn Graph (CCDG). Then it uses the succinct CCDG to genotype any list of phased or unphased variants, leveraging the population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art with unprecedented performance. It took 100 hours to genotype 4.5M variants in 4.2K whole genome human samples using one server with 32 cores and 145GB of memory.