GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. V...

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Detalles Bibliográficos
Autores principales:	Cooke, T. F., Yee, M.-C., Muzzio, Marina, Sockell, A., Bell, R., Cornejo, O. E., Kelley, J. L., Bailliet, Graciela, Bravi, Claudio Marcelo, Bustamante, Carlos D., Kenny, E. E.
Formato:	Articulo
Lenguaje:	Inglés
Publicado:	2016
Materias:	Ciencias Exactas GBS genetic variation
Acceso en línea:	http://sedici.unlp.edu.ar/handle/10915/87069
Aporte de:	SEDICI (UNLP) de Universidad Nacional de La Plata

id	I19-R120-10915-87069
record_format	dspace
institution	Universidad Nacional de La Plata
institution_str	I-19
repository_str	R-120
collection	SEDICI (UNLP)
language	Inglés
topic	Ciencias Exactas GBS genetic variation
spellingShingle	Ciencias Exactas GBS genetic variation Cooke, T. F. Yee, M.-C. Muzzio, Marina Sockell, A. Bell, R. Cornejo, O. E. Kelley, J. L. Bailliet, Graciela Bravi, Claudio Marcelo Bustamante, Carlos D. Kenny, E. E. GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
topic_facet	Ciencias Exactas GBS genetic variation
description	Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.
format	Articulo Articulo
author	Cooke, T. F. Yee, M.-C. Muzzio, Marina Sockell, A. Bell, R. Cornejo, O. E. Kelley, J. L. Bailliet, Graciela Bravi, Claudio Marcelo Bustamante, Carlos D. Kenny, E. E.
author_facet	Cooke, T. F. Yee, M.-C. Muzzio, Marina Sockell, A. Bell, R. Cornejo, O. E. Kelley, J. L. Bailliet, Graciela Bravi, Claudio Marcelo Bustamante, Carlos D. Kenny, E. E.
author_sort	Cooke, T. F.
title	GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
title_short	GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
title_full	GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
title_fullStr	GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
title_full_unstemmed	GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
title_sort	gbstools: a statistical method for estimating allelic dropout in reduced representation sequencing data
publishDate	2016
url	http://sedici.unlp.edu.ar/handle/10915/87069
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bdutipo_str	Repositorios
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GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

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