Introduction

Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes.Code in Python is at http://bioinform.github.io/metasv/.rd@bina.comSupplementary data are available at Bioinformatics online.

Publications

  1. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
    Cite this
    Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY, 2015-08-01 - Bioinformatics (Oxford, England)

Credits

  1. Marghoob Mohiyuddin
    Developer

    Bina Technologies, Roche Sequencing, United States of America

  2. John C Mu
    Developer

    Bina Technologies, Roche Sequencing, United States of America

  3. Jian Li
    Developer

    Bina Technologies, Roche Sequencing, United States of America

  4. Narges Bani Asadi
    Developer

    Bina Technologies, Roche Sequencing, United States of America

  5. Mark B Gerstein
    Developer

    Program in Computational Biology and Bioinformatics, Yale University, United States of America

  6. Alexej Abyzov
    Developer

    Department of Health Sciences Research, Center for Individualized Medicine, United States of America

  7. Wing H Wong
    Developer

    Department of Statistics, Stanford University, United States of America

  8. Hugo Y K Lam
    Investigator

    Bina Technologies, Roche Sequencing, United States of America

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Summary
AccessionBT006459
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByHugo Y K Lam