{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T00:38:15Z","timestamp":1782261495406,"version":"3.54.5"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,4,4]],"date-time":"2021-04-04T00:00:00Z","timestamp":1617494400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["5U01MH 109499-04"],"award-info":[{"award-number":["5U01MH 109499-04"]}]},{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["16\/SPP\/3324"],"award-info":[{"award-number":["16\/SPP\/3324"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Next-generation sequencing studies are dependent on a high-quality reference genome for single nucleotide variant (SNV) calling. Although the two most recent builds of the human genome are widely used, position information is typically not directly comparable between them. Re-alignment gives the most accurate position information, but this procedure is often computationally expensive, and therefore, tools such as liftOver and CrossMap are used to convert data from one build to another. However, the positions of converted SNVs do not always match SNVs derived from aligned data, and in some instances, SNVs are known to change chromosome when converted. This is a significant problem when compiling sequencing resources or comparing results across studies. Here, we describe a novel algorithm to identify positions that are unstable when converting between human genome reference builds. These positions are detected independent of the conversion tools and are determined by the chain files, which provide a mapping of contiguous positions from one build to another. We also provide the list of unstable positions for converting between the two most commonly used builds GRCh37 and GRCh38. Pre-excluding SNVs at these positions, prior to conversion, results in SNVs that are stable to conversion. This simple procedure gives the same final list of stable SNVs as applying the algorithm and subsequently removing variants at unstable positions. This work highlights the care that must be taken when converting SNVs between genome builds and provides a simple method for ensuring higher confidence converted data. Unstable positions and algorithm code, available at https:\/\/github.com\/cathaloruaidh\/genomeBuildConversion<\/jats:p>","DOI":"10.1093\/bib\/bbab069","type":"journal-article","created":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T20:11:30Z","timestamp":1614370290000},"source":"Crossref","is-referenced-by-count":34,"title":["Converting single nucleotide variants between genome builds: from cautionary tale to solution"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5717-0508","authenticated-orcid":false,"given":"Cathal","family":"Ormond","sequence":"first","affiliation":[{"name":"Neuropsychiatric Genetics Research Group in the Department of Psychiatry, Trinity College Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9773-2248","authenticated-orcid":false,"given":"Niamh M","family":"Ryan","sequence":"additional","affiliation":[{"name":"Neuropsychiatric Genetics Research Group in the Department of Psychiatry, Trinity College Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6717-4089","authenticated-orcid":false,"given":"Aiden","family":"Corvin","sequence":"additional","affiliation":[{"name":"Neuropsychiatric Genetics Research Group and the Head of the Department of Psychiatry, Trinity College Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2219-4005","authenticated-orcid":false,"given":"Elizabeth A","family":"Heron","sequence":"additional","affiliation":[{"name":"Neuropsychiatric Genetics Research Group in the Department of Psychiatry, Trinity College Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,4,5]]},"reference":[{"issue":"1","key":"2021090815330669000_ref1","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrg3117","article-title":"Repetitive DNA and next-generation sequencing: computational challenges and solutions","volume":"13","author":"Treangen","year":"2011","journal-title":"Nat Rev Genet"},{"issue":"7","key":"2021090815330669000_ref2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001091","article-title":"Modernizing reference genome assemblies","volume":"9","author":"Church","year":"2011","journal-title":"PLoS Biol"},{"issue":"D1","key":"2021090815330669000_ref3","doi-asserted-by":"crossref","first-page":"D853","DOI":"10.1093\/nar\/gky1095","article-title":"The UCSC genome browser database: 2019 update","volume":"47","author":"Haeussler","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021090815330669000_ref4","author":"Genome Reference Consortium","year":"2013"},{"issue":"5","key":"2021090815330669000_ref5","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nmeth0510-331","article-title":"E pluribus unum","volume":"7","year":"2010","journal-title":"Nature Methods"},{"issue":"5","key":"2021090815330669000_ref6","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"Schneider","year":"2017","journal-title":"Genome Res"},{"issue":"2","key":"2021090815330669000_ref7","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ygeno.2017.01.005","article-title":"Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis","volume":"109","author":"Guo","year":"2017","journal-title":"Genomics"},{"issue":"7","key":"2021090815330669000_ref8","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1093\/bioinformatics\/btt730","article-title":"Cross Map: a versatile tool for coordinate conversion between genome assemblies","volume":"30","author":"Zhao","year":"2013","journal-title":"Bioinformatics"},{"issue":"D1","key":"2021090815330669000_ref9","doi-asserted-by":"crossref","first-page":"D8","DOI":"10.1093\/nar\/gkx1095","article-title":"Database resources of the National Center for Biotechnology Information","volume":"46","author":"NCBI","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2021090815330669000_ref10","first-page":"531210","author":"Karczewski","year":"2019"},{"issue":"D1","key":"2021090815330669000_ref11","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gky1016","article-title":"CADD: predicting the deleteriousness of variants throughout the human genome","volume":"47","author":"Rentzsch","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2021090815330669000_ref12","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/humu.22932","article-title":"Db NSFP v3.0: a one-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs","volume":"37","author":"Liu","year":"2016","journal-title":"Hum Mutat"},{"issue":"Suppl 2","key":"2021090815330669000_ref13","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s12859-019-2620-0","article-title":"Similarities and differences between variants called with human reference genome HG19 or HG38","volume":"20","author":"Pan","year":"2019","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2021090815330669000_ref14","doi-asserted-by":"crossref","DOI":"10.1093\/nargab\/lqaa054","article-title":"Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data","volume":"2","author":"Luu","year":"2020","journal-title":"NAR Genomics and Bioinformatics"},{"key":"2021090815330669000_ref15","first-page":"42","article-title":"GNU parallel-the command-line power tool","author":"Tange","year":"2011"},{"issue":"6","key":"2021090815330669000_ref16","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"2021090815330669000_ref17","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1101\/gr.210500.116","article-title":"A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree","volume":"27","author":"Eberle","year":"2017","journal-title":"Genome Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/5\/bbab069\/40260861\/bbab069.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/5\/bbab069\/40260861\/bbab069.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T18:58:55Z","timestamp":1631127535000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbab069\/6210068"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,5]]},"references-count":17,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab069","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9]]},"published":{"date-parts":[[2021,4,5]]},"article-number":"bbab069"}}