Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

Kristian Hanghøj; Ida Moltke; Philip Alstrup Andersen; Andrea Manica; Thorfinn Sand Korneliussen

doi:10.1093/gigascience/giz034

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

Gigascience. 2019 May 1;8(5):giz034. doi: 10.1093/gigascience/giz034.

Authors

Kristian Hanghøj^{1

2}, Ida Moltke³, Philip Alstrup Andersen³, Andrea Manica⁴, Thorfinn Sand Korneliussen^{1

4}

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark.
² Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France.
³ Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
⁴ Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.

Abstract

Background: The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data.

Results: We introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process.

Conclusion: The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).

Keywords: Jacquard coefficients; genotype likelihood; high-throughput sequencing data; inbreeding; next-generation sequencing; population genetics; relatedness estimation; threading.

Publication types

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

MeSH terms

Genetics, Population*
Genotype
Genotyping Techniques*
High-Throughput Nucleotide Sequencing*
Humans
Inbreeding*
Polymorphism, Single Nucleotide / genetics
Sequence Analysis, DNA
Software