{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:40Z","timestamp":1772138080503,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Advances in sequencing capacity have led to the generation of unprecedented amounts of genomic data. The processing of this data frequently leads to I\/O bottlenecks, e. g. when analyzing a small genomic region across a large number of samples. The largest I\/O burden is, however, often not imposed by the amount of data needed for the analysis but rather by index files that help retrieving this data. We have developed chopBAI, a program that can chop a BAM index (BAI) file into small pieces. The program outputs a list of BAI files each indexing a specified genomic interval. The output files are much smaller in size but maintain compatibility with existing software tools. We show how preprocessing BAI files with chopBAI can lead to a reduction of I\/O by more than 95% during the analysis of 10\u2009kb genomic regions, eventually enabling the joint analysis of more than 10 000 individuals.<\/jats:p>\n                  <jats:p>Availability and Implementation: The software is implemented in C\u2009++, GPL licensed and available at http:\/\/github.com\/DecodeGenetics\/chopBAI<\/jats:p>\n                  <jats:p>Contact: \u00a0birte.kehr@decode.is<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw149","type":"journal-article","created":{"date-parts":[[2016,3,18]],"date-time":"2016-03-18T21:40:00Z","timestamp":1458337200000},"page":"2202-2204","source":"Crossref","is-referenced-by-count":0,"title":["chopBAI: BAM index reduction solves I\/O bottlenecks in the joint analysis of large sequencing cohorts"],"prefix":"10.1093","volume":"32","author":[{"given":"Birte","family":"Kehr","sequence":"first","affiliation":[{"name":"1 deCODE Genetics\/Amgen, Reykjav\u00edk, Iceland"}]},{"given":"P\u00e1ll","family":"Melsted","sequence":"additional","affiliation":[{"name":"1 deCODE Genetics\/Amgen, Reykjav\u00edk, Iceland"},{"name":"2 Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjav\u00edk, Iceland"}]}],"member":"286","published-online":{"date-parts":[[2016,3,18]]},"reference":[{"key":"2023020112455317900_btw149-B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1093\/bioinformatics\/btv273","article-title":"PopIns: population-scale detection of novel sequence insertions","volume":"32","author":"Kehr","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112455317900_btw149-B2","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023020112455317900_btw149-B3","author":"Li","year":"2013"},{"key":"2023020112455317900_btw149-B4","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020112455317900_btw149-B5","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/14\/2202\/49020069\/bioinformatics_32_14_2202.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/14\/2202\/49020069\/bioinformatics_32_14_2202.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T17:26:55Z","timestamp":1675272415000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/14\/2202\/1742831"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,18]]},"references-count":5,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2016,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw149","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/030825","asserted-by":"object"}]},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,7,15]]},"published":{"date-parts":[[2016,3,18]]}}}