{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T02:11:24Z","timestamp":1768270284335,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,11,6]],"date-time":"2020-11-06T00:00:00Z","timestamp":1604620800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100010470","name":"Gillson Longenbaugh Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010470","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001064","name":"The Cullen Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001064","id-type":"DOI","asserted-by":"publisher"}]},{"name":"St. Baldrick\u2019s Innovation Award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high-throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and documentation including a tutorial can be accessed at\u00a0https:\/\/github.com\/rghu\/reconCNV as well as a Docker image at https:\/\/hub.docker.com\/repository\/docker\/raghuc1990\/reconcnv.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa746","type":"journal-article","created":{"date-parts":[[2020,8,18]],"date-time":"2020-08-18T04:53:01Z","timestamp":1597726381000},"page":"1164-1167","source":"Crossref","is-referenced-by-count":9,"title":["reconCNV: interactive visualization of copy number data from high-throughput sequencing"],"prefix":"10.1093","volume":"37","author":[{"given":"Raghu","family":"Chandramohan","sequence":"first","affiliation":[{"name":"Department of Molecular and Human Genetics , Houston, TX 77030, USA"}]},{"given":"Nipun","family":"Kakkar","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Texas Children\u2019s Cancer Center , Houston, TX 77030, USA"}]},{"given":"Angshumoy","family":"Roy","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Texas Children\u2019s Cancer Center , Houston, TX 77030, USA"},{"name":"Department of Pathology and Immunology, Baylor College of Medicine , Houston, TX 77030, USA"},{"name":"Department of Pathology, Texas Children\u2019s Hospital , Houston, TX 77030, USA"},{"name":"Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"given":"D Williams","family":"Parsons","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics , Houston, TX 77030, USA"},{"name":"Department of Pediatrics, Texas Children\u2019s Cancer Center , Houston, TX 77030, USA"},{"name":"Department of Pathology and Immunology, Baylor College of Medicine , Houston, TX 77030, USA"},{"name":"Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,11,6]]},"reference":[{"key":"2023051612063159300_btaa746-B1","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/nrg2149","article-title":"Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability","volume":"8","author":"Beckmann","year":"2007","journal-title":"Nat. Rev. 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