{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:14:39Z","timestamp":1773274479076,"version":"3.50.1"},"reference-count":8,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T00:00:00Z","timestamp":1491523200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000092","name":"U.S. National Library of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01-HG006677"],"award-info":[{"award-number":["R01-HG006677"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["DBI-1350041"],"award-info":[{"award-number":["DBI-1350041"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    Over recent years, multiple groups have shown that a large number of structural variants, repeats, or problems with the underlying genome assembly have dramatic effects on the mapping, calling, and overall reliability of single nucleotide polymorphism calls. This project endeavored to develop an easy-to-use track for looking at structural variant and repeat regions. This track, DangerTrack, can be displayed alongside the existing Genome Reference Consortium assembly tracks to warn clinicians and biologists when variants of interest may be incorrectly called, of dubious quality, or on an insertion or copy number expansion. While mapping and variant calling can be automated, it is our opinion that when these regions are of interest to a particular clinical or research group, they warrant a careful examination, potentially involving localized reassembly. DangerTrack is available at\n                    <ns4:ext-link xmlns:ns3=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns3:href=\"https:\/\/github.com\/DCGenomics\/DangerTrack\">https:\/\/github.com\/DCGenomics\/DangerTrack<\/ns4:ext-link>\n                    .\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.11254.1","type":"journal-article","created":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T04:15:11Z","timestamp":1491538511000},"page":"443","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["DangerTrack: A scoring system to detect difficult-to-assess regions"],"prefix":"10.12688","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4451-126X","authenticated-orcid":false,"given":"Igor","family":"Dolgalev","sequence":"first","affiliation":[]},{"given":"Fritz","family":"Sedlazeck","sequence":"additional","affiliation":[]},{"given":"Ben","family":"Busby","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"3207-3212","DOI":"10.1093\/bioinformatics\/btp579","article-title":"Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.","volume":"25","author":"J Degner","year":"2009","journal-title":"Bioinformatics."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"682-688","DOI":"10.1038\/ng.3257","article-title":"Improved genome inference in the MHC using a population reference graph.","volume":"47","author":"A Dilthey","year":"2015","journal-title":"Nat 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Satya","year":"2012","journal-title":"Nucleic Acides Res."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"75-81","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes.","volume":"526","author":"P Sudmant","year":"2015","journal-title":"Nature."},{"key":"ref-8","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.25","article-title":"Extensive sequencing of seven human genomes to characterize benchmark reference materials.","volume":"3","author":"J Zook","year":"2016","journal-title":"Sci 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.12141.r21625, Melissa A. Gymrek, Nima Mousavi, Department of Medicine, University of California, San Diego, La Jolla, CA, USA, 24 Apr 2017, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/6-443\/v1#referee-response-21625","order":0,"name":"referee-response-21625","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.12141.r21624, Justin M. Zook, Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA, 24 Apr 2017, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/6-443\/v1#referee-response-21624","order":1,"name":"referee-response-21624","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.12141.r21627, Andrew Carroll, DNAnexus, Mountain View, CA, USA, 24 Apr 2017, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/6-443\/v1#referee-response-21627","order":2,"name":"referee-response-21627","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"F.S. was supported through a National Science Foundation award (DBI-1350041) and National Institutes of Health award (R01-HG006677). B.B. was supported by the Intramural Research Program of the National Library of Medicine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Data associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).","order":0,"name":"copyright-info","label":"Copyright"}]}}