{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T23:27:31Z","timestamp":1775690851626,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":541,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>Availability and implementation: Code in Python is at http:\/\/bioinform.github.io\/metasv\/.<\/jats:p>\n               <jats:p>Contact: \u00a0rd@bina.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv204","type":"journal-article","created":{"date-parts":[[2015,4,11]],"date-time":"2015-04-11T03:32:53Z","timestamp":1428723173000},"page":"2741-2744","source":"Crossref","is-referenced-by-count":158,"title":["MetaSV: an accurate and integrative structural-variant caller for next generation sequencing"],"prefix":"10.1093","volume":"31","author":[{"given":"Marghoob","family":"Mohiyuddin","sequence":"first","affiliation":[{"name":"1 Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John C.","family":"Mu","sequence":"additional","affiliation":[{"name":"1 Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Li","sequence":"additional","affiliation":[{"name":"1 Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Narges","family":"Bani Asadi","sequence":"additional","affiliation":[{"name":"1 Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark B.","family":"Gerstein","sequence":"additional","affiliation":[{"name":"2 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexej","family":"Abyzov","sequence":"additional","affiliation":[{"name":"3 Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wing H.","family":"Wong","sequence":"additional","affiliation":[{"name":"4 Department of Statistics, Stanford University, Stanford, CA 94035, USA and"},{"name":"5 Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugo Y.K.","family":"Lam","sequence":"additional","affiliation":[{"name":"1 Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,4,10]]},"reference":[{"key":"2023020202200794200_btv204-B1","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1093\/bioinformatics\/btq713","article-title":"AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision","volume":"27","author":"Abyzov","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020202200794200_btv204-B2","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"2023020202200794200_btv204-B3","doi-asserted-by":"crossref","first-page":"7256","DOI":"10.1038\/ncomms8256","article-title":"Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms","volume":"6","author":"Abyzov","year":"2015","journal-title":"Nat. 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