MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y K Lam

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

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. Availability and implementation: Code in Python is at http://bioinform.github.io/metasv/.

Original languageEnglish (US)
Pages (from-to)2741-2744
Number of pages4
JournalBioinformatics
Volume31
Issue number16
DOIs
StatePublished - Jan 19 2015

Fingerprint

Sequencing
Genomic Structural Variation
Boidae
Dynamic programming
Merging
Genotype
Availability
Insertion
Genomic Rearrangements
Python
Leverage
Dynamic Programming
High Accuracy
Alignment
Coverage
High Resolution
Experimental Data
Vary
Predict
Demonstrate

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Mohiyuddin, M., Mu, J. C., Li, J., Bani Asadi, N., Gerstein, M. B., Abyzov, A., ... Lam, H. Y. K. (2015). MetaSV: An accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics, 31(16), 2741-2744. https://doi.org/10.1093/bioinformatics/btv204

MetaSV : An accurate and integrative structural-variant caller for next generation sequencing. / Mohiyuddin, Marghoob; Mu, John C.; Li, Jian; Bani Asadi, Narges; Gerstein, Mark B.; Abyzov, Alexej; Wong, Wing H.; Lam, Hugo Y K.

In: Bioinformatics, Vol. 31, No. 16, 19.01.2015, p. 2741-2744.

Research output: Contribution to journalArticle

Mohiyuddin, M, Mu, JC, Li, J, Bani Asadi, N, Gerstein, MB, Abyzov, A, Wong, WH & Lam, HYK 2015, 'MetaSV: An accurate and integrative structural-variant caller for next generation sequencing', Bioinformatics, vol. 31, no. 16, pp. 2741-2744. https://doi.org/10.1093/bioinformatics/btv204
Mohiyuddin, Marghoob ; Mu, John C. ; Li, Jian ; Bani Asadi, Narges ; Gerstein, Mark B. ; Abyzov, Alexej ; Wong, Wing H. ; Lam, Hugo Y K. / MetaSV : An accurate and integrative structural-variant caller for next generation sequencing. In: Bioinformatics. 2015 ; Vol. 31, No. 16. pp. 2741-2744.
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