skater: an R package for SNP-based kinship analysis, testing, and evaluation

Stephen D Turner; V P Nagraj; Matthew Scholz; Shakeel Jessa; Carlos Acevedo; Jianye Ge; August E Woerner; Bruce Budowle

doi:10.12688/f1000research.76004.1

skater: an R package for SNP-based kinship analysis, testing, and evaluation

F1000Res. 2022 Jan 7:11:18. doi: 10.12688/f1000research.76004.1. eCollection 2022.

Authors

Stephen D Turner¹, V P Nagraj¹, Matthew Scholz¹, Shakeel Jessa¹, Carlos Acevedo¹, Jianye Ge², August E Woerner², Bruce Budowle²

Affiliations

¹ Signature Science, LLC., Austin, TX, 78759, USA.
² Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.

Abstract

Motivation: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream process- ing and manipulation. A dedicated software package that consistently and intuitively imple- ments this analysis functionality is needed. Results: Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data. Availability: The skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.

Keywords: R; SNPs; bioinformatics; genealogy; kinship; relatedness; single nucleotide polymorphisms.

Publication types

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

MeSH terms

Computational Biology
Genome*
Humans
Pedigree*
Polymorphism, Single Nucleotide*
Software

Grants and funding

This work was supported in part by award 2019-DU-BX-0046 (Dense DNA Data for Enhanced Missing Persons Identification) to B.B., awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice and by internal funds from the Center for Human Identification. The opinions, findings, and conclusions or recommendations expressed are those of the authors and do not necessarily reflect those of the U.S. Department of Justice.