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