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skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation

View ORCID ProfileStephen D. Turner, View ORCID ProfileV.P. Nagraj, View ORCID ProfileMatthew Scholz, Shakeel Jessa, Carlos Acevedo, View ORCID ProfileJianye Ge, View ORCID ProfileAugust E. Woerner, View ORCID ProfileBruce Budowle
doi: https://doi.org/10.1101/2021.07.21.453083
Stephen D. Turner
1Signature Science, LLC., Austin, TX 78759, USA
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  • For correspondence: sturner@signaturescience.com
V.P. Nagraj
1Signature Science, LLC., Austin, TX 78759, USA
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Matthew Scholz
1Signature Science, LLC., Austin, TX 78759, USA
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Shakeel Jessa
1Signature Science, LLC., Austin, TX 78759, USA
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Carlos Acevedo
1Signature Science, LLC., Austin, TX 78759, USA
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Jianye Ge
2Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
3Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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August E. Woerner
2Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
3Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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Bruce Budowle
2Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
3Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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Abstract

Motivation SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream processing and manipulation. A dedicated software package that consistently and intuitively implements 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.

Contact sturner{at}signaturescience.com

Supplementary information Supplementary data are available at Bioinformatics Online.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/signaturescience/skater

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 22, 2021.
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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
bioRxiv 2021.07.21.453083; doi: https://doi.org/10.1101/2021.07.21.453083
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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
bioRxiv 2021.07.21.453083; doi: https://doi.org/10.1101/2021.07.21.453083

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