{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:22Z","timestamp":1753875742098,"version":"3.41.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T00:00:00Z","timestamp":1721174400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U24CA220242","U24CA258406"],"award-info":[{"award-number":["U24CA220242","U24CA258406"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["UG3NS132128"],"award-info":[{"award-number":["UG3NS132128"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Individualized Medicine at Mayo Clinic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Copy number variation (CNV) and alteration (CNA) analysis is a crucial component in many genomic studies and its applications span from basic research to clinic diagnostics and personalized medicine. CNVpytor is a tool featuring a read depth-based caller and combined read depth and B-allele frequency (BAF) based 2D caller to find CNVs and CNAs. The tool stores processed intermediate data and CNV\/CNA calls in a compact HDF5 file\u2014pytor file. Here, we describe a new track in igv.js that utilizes pytor and whole genome variant files as input for on-the-fly read depth and BAF visualization, CNV\/CNA calling and analysis. Embedding into HTML pages and Jupiter Notebooks enables convenient remote data access and visualization simplifying interpretation and analysis of omics data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The CNVpytor track is integrated with igv.js and available at https:\/\/github.com\/igvteam\/igv.js. The documentation is available at https:\/\/github.com\/igvteam\/igv.js\/wiki\/cnvpytor. Usage can be tested in the IGV-Web app at https:\/\/igv.org\/app and also on https:\/\/github.com\/abyzovlab\/CNVpytor.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae453","type":"journal-article","created":{"date-parts":[[2024,7,16]],"date-time":"2024-07-16T05:21:26Z","timestamp":1721107286000},"source":"Crossref","is-referenced-by-count":1,"title":["Genome-wide analysis and visualization of copy number with CNVpytor in igv.js"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5156-6459","authenticated-orcid":false,"given":"Arijit","family":"Panda","sequence":"first","affiliation":[{"name":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5839-9611","authenticated-orcid":false,"given":"Milovan","family":"Suvakov","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States"}]},{"given":"Helga","family":"Thorvaldsdottir","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"}]},{"given":"Jill P","family":"Mesirov","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States"},{"name":"Moores Cancer Center, University of California San Diego , La Jolla, CA 92037, United States"}]},{"given":"James T","family":"Robinson","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5405-6729","authenticated-orcid":false,"given":"Alexej","family":"Abyzov","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , 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