Nov 3, 2015

GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping

BioRxiv : the Preprint Server for Biology
Thomas F CookeEimear E Kenny

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 populatio...Continue Reading

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Mentioned in this Paper

Computer Software
Gene Polymorphism
Genome
Restriction Site
Genome Assembly Sequence
Nucleic Acid Sequencing
Etiology
Genetic Activator
Genomics
Sequencing

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