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graphtyper website  

graphtyper is a graph-based variant caller capable of genotyping population-scale short read data sets. It represents a reference genome and known variants of a genomic region using an acyclic graph structure (a "pangenome reference"), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs, small indels, and structural variants.

Environment Modules

Run module spider graphtyper to find out what environment modules are available for this application.

System Variables

  • HPC_GRAPHTYPER_DIR - installation directory
  • HPC_GRAPHTYPER_BIN - executable directory


If you publish research that uses graphtyper you have to cite it as follows:

Hannes P. Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E. Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F. Gudbjartsson, Pall Melsted, Kari Stefansson, Bjarni V. Halldorsson. Graphtyper enables population-scale genotyping using pangenome graphs. Nature Genetics 49, 1654–1660 (2017). doi:10.1038/ng.3964

Eggertsson, H.P., Kristmundsdottir, S., Beyter, D. et al. GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs. Nature Communications 10, 5402 (2019) doi:10.1038/s41467-019-13341-9