{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:21:33Z","timestamp":1760170893468},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,11,19]],"date-time":"2014-11-19T00:00:00Z","timestamp":1416355200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0359-1","type":"journal-article","created":{"date-parts":[[2014,11,18]],"date-time":"2014-11-18T20:03:38Z","timestamp":1416341018000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Vindel: a simple pipeline for checking indel redundancy"],"prefix":"10.1186","volume":"15","author":[{"given":"Zhiyi","family":"Li","sequence":"first","affiliation":[]},{"given":"Xiaowei","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Bin","family":"He","sequence":"additional","affiliation":[]},{"given":"Liqing","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"issue":"7422","key":"359_CR1","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nature11632","volume":"491","author":"GR Abecasis","year":"2012","unstructured":"Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1,092 human genomes. Nature. 2012, 491 (7422): 56-65. 10.1038\/nature11632.","journal-title":"Nature"},{"key":"359_CR2","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1101\/gr.115907.110","volume":"21","author":"E Ryan","year":"2011","unstructured":"Ryan E, Mills WSP: Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res. 2011, 21: 830-839. 10.1101\/gr.115907.110.","journal-title":"Genome Res"},{"key":"359_CR3","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1186\/1471-2164-13-440","volume":"13","author":"AR Rivi Gupta","year":"2012","unstructured":"Rivi Gupta AR: Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012, 13: 440-10.1186\/1471-2164-13-440.","journal-title":"BMC Genomics"},{"issue":"11","key":"359_CR4","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18 (11): 1851-1858. 10.1101\/gr.078212.108.","journal-title":"Genome Res"},{"issue":"3","key":"359_CR5","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186\/gb-2009-10-3-r25.","journal-title":"Genome Biol"},{"issue":"11","key":"359_CR6","doi-asserted-by":"publisher","first-page":"A95","DOI":"10.1371\/journal.pone.0007767","volume":"4","author":"N Homer","year":"2009","unstructured":"Homer N, Merriman B, Nelson SF: BFAST: an alignment tool for large scale genome resequencing. PLoS One. 2009, 4 (11): A95-A106. 10.1371\/journal.pone.0007767.","journal-title":"PLoS One"},{"issue":"7","key":"359_CR7","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.1093\/bioinformatics\/btr046","volume":"27","author":"M David","year":"2011","unstructured":"David M, Dzamba M, Lister D, Ilie L, Brudno M: SHRiMP2: sensitive yet practical short read mapping. Bioinformatics. 2011, 27 (7): 1011-1012. 10.1093\/bioinformatics\/btr046.","journal-title":"Bioinformatics"},{"issue":"14","key":"359_CR8","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"key":"359_CR9","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/1471-2164-14-132","volume":"14","author":"D Grimm","year":"2013","unstructured":"Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K: Accurate indel prediction using paired-end short reads. BMC Genomics. 2013, 14: 132-10.1186\/1471-2164-14-132.","journal-title":"BMC Genomics"},{"issue":"21","key":"359_CR10","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","volume":"25","author":"K Ye","year":"2009","unstructured":"Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009, 25 (21): 2865-2871. 10.1093\/bioinformatics\/btp394.","journal-title":"Bioinformatics"},{"issue":"23","key":"359_CR11","doi-asserted-by":"publisher","first-page":"3228","DOI":"10.1093\/bioinformatics\/btr563","volume":"27","author":"J Zhang","year":"2011","unstructured":"Zhang J, Wu Y: SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. Bioinformatics. 2011, 27 (23): 3228-3234. 10.1093\/bioinformatics\/btr563.","journal-title":"Bioinformatics"},{"issue":"5","key":"359_CR12","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1093\/bioinformatics\/btq713","volume":"27","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Gerstein M: AGE: defining breakpoints of genomic structural variants at single- nucleotide resolution, through optimal alignments with gap excision. Bioinformatics. 2011, 27 (5): 595-603. 10.1093\/bioinformatics\/btq713.","journal-title":"Bioinformatics"},{"issue":"6","key":"359_CR13","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1101\/gr.112326.110","volume":"21","author":"CA Albers","year":"2011","unstructured":"Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R: Dindel: accurate indel calls from short-read data. Genome Res. 2011, 21 (6): 961-973. 10.1101\/gr.112326.110.","journal-title":"Genome Res"},{"issue":"5","key":"359_CR14","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011, 43 (5): 491-498. 10.1038\/ng.806.","journal-title":"Nat Genet"},{"issue":"4","key":"359_CR15","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1007\/BF00164032","volume":"40","author":"XLW Gu","year":"1995","unstructured":"Gu XLW: The size distribution of insertions and deletions in human ad rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J Mol Evol. 1995, 40 (4): 464-473. 10.1007\/BF00164032.","journal-title":"J Mol Evol"},{"key":"359_CR16","volume-title":"Power Laws, Scale-Free Networks and Genome Biology","author":"M Kamal NL","year":"2006","unstructured":"Kamal NL M: Power Laws, Scale-Free Networks and Genome Biology. 2006, Springer, New York, New York"},{"issue":"4","key":"359_CR17","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1080\/07350015.1995.10524620","volume":"13","author":"R Winkelmann","year":"1995","unstructured":"Winkelmann R: Duration dependence and dispersion in count-data models. J Bus Econ Stat. 1995, 13 (4): 467-474.","journal-title":"J Bus Econ Stat"},{"issue":"3","key":"359_CR18","first-page":"225","volume":"11","author":"CT S. V. Lekshmi","year":"2012","unstructured":"S. V. Lekshmi CT: Some generalization of poisson processes. J Stat Theor Appl. 2012, 11 (3): 225-235.","journal-title":"J Stat Theor Appl"},{"issue":"3","key":"359_CR19","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/genetics\/133.3.681","volume":"133","author":"E Foss","year":"1993","unstructured":"Foss E, Lande R, Stahl FW, Steinberg CM: Chiasma interference as a function of genetic-distance. Genetics. 1993, 133 (3): 681-691.","journal-title":"Genetics"},{"issue":"2","key":"359_CR20","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1093\/genetics\/139.2.1031","volume":"139","author":"MS Mcpeek","year":"1995","unstructured":"Mcpeek MS, Speed TP: Modeling interference in genetic-recombination. Genetics. 1995, 139 (2): 1031-1044.","journal-title":"Genetics"},{"issue":"7146","key":"359_CR21","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng ZP, Snyder M, Dermitzakis ET, Stamatoyannopoulos JA, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038\/nature05874.","journal-title":"Nature"},{"issue":"7431","key":"359_CR22","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1038\/nature11690","volume":"493","author":"WQ Fu","year":"2013","unstructured":"Fu WQ, O\u2019Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Exome Sequencing Project NHLBI, Akey JM: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013, 493 (7431): 216-220. 10.1038\/nature11690.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0359-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0359-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0359-1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0359-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,5]],"date-time":"2024-06-05T04:33:04Z","timestamp":1717561984000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0359-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,19]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["359"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0359-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,19]]},"assertion":[{"value":"28 June 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 October 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"359"}}