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. 2015 Aug 15;31(16):2741-4.
doi: 10.1093/bioinformatics/btv204. Epub 2015 Apr 10.

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

Marghoob Mohiyuddin  1 , John C Mu  1 , Jian Li  1 , Narges Bani Asadi  1 , Mark B Gerstein  2 , Alexej Abyzov  3 , Wing H Wong  4 , Hugo Y K Lam  1
Affiliations

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

Marghoob Mohiyuddin et al. Bioinformatics. .

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/.

Contact: rd@bina.com

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
High-level view of the MetaSV methodology
Fig. 2.
Fig. 2.
Accuracy comparisons for deletions and insertions. Accuracy metrics are shown on a per size bin basis in the plots. The tables below the plots show the aggregate accuracy scores. If a tool does not support detecting the SV type, an NA is indicated in the table. Each tool name is color coded to match the color code in the plots. DELLY’s suboptimal deletion performance was due to its lower breakpoint resolution. For insertions, although Pindel’s sensitivity was close to MetaSV, it had a significantly lower precision and overall accuracy
See this image and copyright information in PMC

References

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