Introduction

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method's ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.

Publications

  1. Inferring short tandem repeat variation from paired-end short reads.
    Cite this
    Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S, Bodén M, 2014-02-01 - Nucleic acids research

Credits

  1. Minh Duc Cao
    Developer

    School of Chemistry and Molecular Biosciences, The University of Queensland, Australia

  2. Edward Tasker
    Developer

  3. Kai Willadsen
    Developer

  4. Michael Imelfort
    Developer

  5. Sailaja Vishwanathan
    Developer

  6. Sridevi Sureshkumar
    Developer

  7. Sureshkumar Balasubramanian
    Developer

  8. Mikael Bodén
    Investigator

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Summary
AccessionBT000307
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMikael Bodén