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GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping

GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping

Authors :
Omar E. Cornejo
Graciela Bailliet
Claudio M. Bravi
Eimear E. Kenny
Joanna L. Kelley
Alexandra Sockell
Ryan T. Bell
Carlos Bustamante
Marina Muzzio
Thomas F. Cooke
Muh-Ching Yee
Publication Year :
2015
Publisher :
Cold Spring Harbor Laboratory, 2015.

Abstract

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.

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....81af6627b300af0a2e5e095c68996f81
Full Text :
https://doi.org/10.1101/030494