title: Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
abstract: Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.
authors.forename: Gareth
authors.initials: G
authors.lastname: Highnam
authors.forename: Christopher
authors.initials: C
authors.lastname: Franck
authors.forename: Andy
authors.initials: A
authors.lastname: Martin
authors.forename: Calvin
authors.initials: C
authors.lastname: Stephens
authors.forename: Ashwin
authors.initials: A
authors.lastname: Puthige
authors.forename: David
authors.initials: D
authors.lastname: Mittelman
mesh_terms: D001499:Bayes Theorem; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D005838:Genotype; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018895:Microsatellite Repeats; D012984:Software