{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T23:38:31Z","timestamp":1777333111249,"version":"3.51.4"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1644,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology.<\/jats:p><jats:p>Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM\/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.<\/jats:p><jats:p>Availability and implementation: Source code and sample data are freely available under GNU license (GPLv3) at http:\/\/contra-cnv.sourceforge.net\/<\/jats:p><jats:p>Contact: \u00a0Jason.Li@petermac.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts146","type":"journal-article","created":{"date-parts":[[2012,4,4]],"date-time":"2012-04-04T00:44:21Z","timestamp":1333500261000},"page":"1307-1313","source":"Crossref","is-referenced-by-count":297,"title":["CONTRA: copy number analysis for targeted resequencing"],"prefix":"10.1093","volume":"28","author":[{"given":"Jason","family":"Li","sequence":"first","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Lupat","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"},{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaushalya C.","family":"Amarasinghe","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ella R.","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria A.","family":"Doyle","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter 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MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saman K.","family":"Halgamuge","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian G.","family":"Campbell","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"},{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"},{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kylie L.","family":"Gorringe","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Core Facility, 2Victorian Breast Cancer Research Consortium Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, VIC 3002, 3Department of Mechanical Engineering, University of Melbourne, Parkville, VIC 3010, 4Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, VIC 3002, 5Sir Peter MacCallum Department of Oncology and 6Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia"},{"name":"1 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