HaploGrouper: a generalized approach to haplogroup classification

Anuradha Jagadeesan; S Sunna Ebenesersdóttir; Valdis B Guðmundsdóttir; Elisabet Linda Thordardottir; Kristjan H S Moore; Agnar Helgason

doi:10.1093/bioinformatics/btaa729

HaploGrouper: a generalized approach to haplogroup classification

Bioinformatics. 2021 May 1;37(4):570-572. doi: 10.1093/bioinformatics/btaa729.

Authors

Anuradha Jagadeesan^{1

2}, S Sunna Ebenesersdóttir^{1

2}, Valdis B Guðmundsdóttir^{1

2}, Elisabet Linda Thordardottir¹, Kristjan H S Moore¹, Agnar Helgason^{1

2}

Affiliations

¹ deCODE Genetics/Amgen, Reykjavik 101, Iceland.
² Department of Anthropology, University of Iceland, Reykjavik 101, Iceland.

PMID: 32805011
DOI: 10.1093/bioinformatics/btaa729

Abstract

Motivation: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.

Results: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.

Availability and implementation: The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA, Mitochondrial* / genetics
Haplotypes / genetics
Humans
Phylogeny
Software*
Y Chromosome

Substances

DNA, Mitochondrial