{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:19Z","timestamp":1740185119820,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,3,27]],"date-time":"2019-03-27T00:00:00Z","timestamp":1553644800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Verily Life Sciences and Google LLC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Reference genomes are refined to reflect error corrections and other improvements. While this process improves novel data generation and analysis, incorporating data analyzed on an older reference genome assembly requires transforming the coordinates and representations of the data to the new assembly. Multiple tools exist to perform this transformation for coordinate-only data types, but none supports accurate transformation of genome-wide short variation. Here we present GenomeWarp, a tool for efficiently transforming variants between genome assemblies. GenomeWarp transforms regions and short variants in a conservative manner to minimize false positive and negative variants in the target genome, and converts over 99% of regions and short variants from a representative human genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GenomeWarp is written in Java. All source code and the user manual are freely available at https:\/\/github.com\/verilylifesciences\/genomewarp.<\/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\/btz218","type":"journal-article","created":{"date-parts":[[2019,3,23]],"date-time":"2019-03-23T20:06:28Z","timestamp":1553371588000},"page":"4389-4391","source":"Crossref","is-referenced-by-count":4,"title":["GenomeWarp: an alignment-based variant coordinate transformation"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9928-8216","authenticated-orcid":false,"given":"Cory Y","family":"McLean","sequence":"first","affiliation":[{"name":"Verily Life Sciences, Mountain View , CA, USA"},{"name":"Google Inc., Mountain View , CA, USA"}]},{"given":"Yeongwoo","family":"Hwang","sequence":"additional","affiliation":[{"name":"Verily Life Sciences, Mountain View , CA, USA"},{"name":"Department of Computer Science, Carnegie Mellon University , Pittsburgh, PA, USA"}]},{"given":"Ryan","family":"Poplin","sequence":"additional","affiliation":[{"name":"Verily Life Sciences, Mountain View , CA, USA"},{"name":"Google Inc., Mountain View , CA, USA"}]},{"given":"Mark A","family":"DePristo","sequence":"additional","affiliation":[{"name":"Verily Life Sciences, Mountain View , CA, USA"},{"name":"Google Inc., Mountain View , CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,3,27]]},"reference":[{"key":"2023062712432870300_btz218-B1","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","year":"2001","journal-title":"Nature"},{"key":"2023062712432870300_btz218-B2","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature03001","article-title":"Finishing the euchromatic sequence of the human genome","volume":"431","year":"2004","journal-title":"Nature"},{"key":"2023062712432870300_btz218-B3","doi-asserted-by":"crossref","first-page":"11484","DOI":"10.1073\/pnas.1932072100","article-title":"Evolution\u2019s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes","volume":"100","author":"Kent","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062712432870300_btz218-B4","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn","year":"2013","journal-title":"Brief. Bioinform"},{"key":"2023062712432870300_btz218-B5","article-title":"GLnexus: joint variant calling for large cohort sequencing","author":"Lin","year":"2018","journal-title":"bioRxiv"},{"key":"2023062712432870300_btz218-B6","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"Poplin","year":"2017","journal-title":"bioRxiv"},{"key":"2023062712432870300_btz218-B7","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"Creating a universal SNP and small indel variant caller with deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat. 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