{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T05:15:43Z","timestamp":1771564543885,"version":"3.50.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,11,19]],"date-time":"2018-11-19T00:00:00Z","timestamp":1542585600000},"content-version":"tdm","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":[[2018,12]]},"DOI":"10.1186\/s12859-018-2440-7","type":"journal-article","created":{"date-parts":[[2018,11,19]],"date-time":"2018-11-19T13:20:33Z","timestamp":1542633633000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Comparing the performance of selected variant callers using synthetic data and genome segmentation"],"prefix":"10.1186","volume":"19","author":[{"given":"Xiaopeng","family":"Bian","sequence":"first","affiliation":[]},{"given":"Bin","family":"Zhu","sequence":"additional","affiliation":[]},{"given":"Mingyi","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Ying","family":"Hu","sequence":"additional","affiliation":[]},{"given":"Qingrong","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Cu","family":"Nguyen","sequence":"additional","affiliation":[]},{"given":"Belynda","family":"Hicks","sequence":"additional","affiliation":[]},{"given":"Daoud","family":"Meerzaman","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,11,19]]},"reference":[{"issue":"9","key":"2440_CR1","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/nrg.2016.86","volume":"17","author":"EA Ashley","year":"2016","unstructured":"Ashley EA. Towards precision medicine. Nat Rev Genet. 2016;17(9):507\u201322.","journal-title":"Nat Rev Genet"},{"key":"2440_CR2","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.ctrv.2017.03.002","volume":"55","author":"N Dey","year":"2017","unstructured":"Dey N, Williams C, Leyland-Jones B, De P. Mutation matters in precision medicine: a future to believe in. Cancer Treat Rev. 2017;55:136\u201349.","journal-title":"Cancer Treat Rev"},{"issue":"11","key":"2440_CR3","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1038\/nbt.2743","volume":"31","author":"JY Park","year":"2013","unstructured":"Park JY, Kricka LJ, Fortina P. Next-generation sequencing in the clinic. Nat Biotechnol. 2013;31(11):990\u20132.","journal-title":"Nat Biotechnol"},{"issue":"7","key":"2440_CR4","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/nmeth.3407","volume":"12","author":"AD Wing","year":"2015","unstructured":"Wing AD, Houlahan KE, Hu Y, Ellrott K, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015;12(7):623\u201330.","journal-title":"Nat Methods"},{"key":"2440_CR5","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.csbj.2018.01.003","volume":"16","author":"C Xu","year":"2018","unstructured":"Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput Struct Biotechnol J. 2018;16:15\u201324.","journal-title":"Comput Struct Biotechnol J"},{"issue":"3","key":"2440_CR6","doi-asserted-by":"publisher","first-page":"e0151664","DOI":"10.1371\/journal.pone.0151664","volume":"11","author":"AB Kr\u00f8ig\u00e5rd","year":"2016","unstructured":"Kr\u00f8ig\u00e5rd AB, Thomassen M, L\u00e6nkholm AV, Kruse TA, Larsen MJ. Evaluation of nine somatic variant callers for detection of somatic mutations in exome and targeted deep sequencing data. PLoS One. 2016;11(3):e0151664.","journal-title":"PLoS One"},{"issue":"10","key":"2440_CR7","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/gm495","volume":"5","author":"Q Wang","year":"2013","unstructured":"Wang Q, Jia P, Li F, Chen H, Ji H a. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med. 2013;5(10):91.","journal-title":"Genome Med"},{"key":"2440_CR8","doi-asserted-by":"publisher","first-page":"36540","DOI":"10.1038\/srep36540","volume":"6","author":"L Cai","year":"2016","unstructured":"Cai L, Yuan W, Zhang Z, He L, Chou KC. In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data. Sci Rep. 2016;6:36540.","journal-title":"Sci Rep"},{"issue":"3","key":"2440_CR9","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nbt.2514","volume":"31","author":"K Cibulskis","year":"2013","unstructured":"Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213\u20139.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"2440_CR10","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s12859-016-1417-7","volume":"18","author":"AL Hofmann","year":"2017","unstructured":"Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics. 2017;18(1):8.","journal-title":"BMC Bioinformatics"},{"key":"2440_CR11","doi-asserted-by":"publisher","first-page":"10001","DOI":"10.1038\/ncomms10001","volume":"6","author":"TS Alioto","year":"2015","unstructured":"Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015;6:10001.","journal-title":"Nat Commun"},{"key":"2440_CR12","doi-asserted-by":"publisher","first-page":"43169","DOI":"10.1038\/srep43169","volume":"7","author":"S Sandmann","year":"2017","unstructured":"Sandmann S, de Graaf AO, Karimi M, van der Reijden BA, Hellstr\u00f6m-Lindberg E, et al. Evaluating variant calling tools for non-matched next-generation sequencing data. Sci Rep. 2017;7:43169.","journal-title":"Sci Rep"},{"key":"2440_CR13","volume-title":"Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN]","author":"E Garrison","year":"2012","unstructured":"Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012."},{"issue":"1","key":"2440_CR14","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s13059-016-1029-6","volume":"17","author":"Y Fan","year":"2016","unstructured":"Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, et al. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biol. 2016;17(1):178.","journal-title":"Genome Biol"},{"issue":"11","key":"2440_CR15","doi-asserted-by":"publisher","first-page":"e108","DOI":"10.1093\/nar\/gkw227","volume":"44","author":"Z Lai","year":"2016","unstructured":"Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res. 2016;44(11):e108.","journal-title":"Nucleic Acids Res"},{"key":"2440_CR16","unstructured":"Description of Synthetic Tumors Generated for the DREAM Challenge. \n                    https:\/\/www.synapse.org\/#!Synapse:syn312572\/wiki\/62018\n                    \n                  ."},{"key":"2440_CR17","unstructured":"GATK resources bundle. \n                    https:\/\/github.com\/bahlolab\/bioinfotools\/blob\/master\/GATK\/resource_bundle.md\n                    \n                  ."},{"key":"2440_CR18","unstructured":"dbSNP resource at NCBI. \n                    https:\/\/www.ncbi.nlm.nih.gov\/snp\n                    \n                  ."},{"key":"2440_CR19","unstructured":"COSMIC resource. \n                    https:\/\/cancer.sanger.ac.uk\/cosmic\n                    \n                  ."},{"key":"2440_CR20","unstructured":"Panel of Normals (PON) at Broad Institute. \n                    https:\/\/gatkforums.broadinstitute.org\/gatk\/discussion\/11053\/panel-of-normals-pon\n                    \n                  ."},{"key":"2440_CR21","unstructured":"Freebayes user guide. \n                    https:\/\/github.com\/ekg\/freebayes#user-manual-and-guide\n                    \n                  ."},{"key":"2440_CR22","unstructured":"VarDict resource. \n                    https:\/\/github.com\/AstraZeneca-NGS\/VarDict\n                    \n                  ."},{"key":"2440_CR23","unstructured":"Mutect at Broad. \n                    https:\/\/software.broadinstitute.org\/cancer\/cga\/mutect\n                    \n                  ."},{"key":"2440_CR24","unstructured":"Mutect2 at Broad. \n                    https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/4.beta.4\/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php\n                    \n                  ."},{"key":"2440_CR25","unstructured":"MuSE resource. \n                    http:\/\/bioinformatics.mdanderson.org\/main\/MuSE\n                    \n                  ."},{"key":"2440_CR26","unstructured":"bcbio-nextgen resource. \n                    http:\/\/bcbio-nextgen.readthedocs.io\/en\/latest\/index.html\n                    \n                  ."},{"key":"2440_CR27","unstructured":"Code for evaluator. \n                    https:\/\/github.com\/Sage-Bionetworks\/SMC-DNA-Meta\/blob\/master\/evaluator.py\n                    \n                  ."},{"key":"2440_CR28","doi-asserted-by":"publisher","first-page":"13","DOI":"10.4137\/CIN.S13495","volume":"13","author":"Y Hu","year":"2014","unstructured":"Hu Y, Yan C, Hsu CH, Chen QR, Niu K, et al. OmicCircos: a simple-to-use R package for the circular visualization of multidimensional omics data. Cancer Inform. 2014;13:13\u201320.","journal-title":"Cancer Inform"},{"key":"2440_CR29","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1479-7364-8-14","volume":"8","author":"M Pirooznia","year":"2014","unstructured":"Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, et al. Validation and assessment of variant calling pipelines for next-generation sequencing. Hum Genomics. 2014;8:14.","journal-title":"Hum Genomics"},{"key":"2440_CR30","unstructured":"Characteristics of the human genome. \n                    https:\/\/courses.cs.washington.edu\/courses\/cse527\/07au\/notes\/notes16.pdf\n                    \n                  ."},{"issue":"3","key":"2440_CR31","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1093\/hmg\/ddi038","volume":"14","author":"Marie S\u00e9mon","year":"2004","unstructured":"S\u00e9mon M1, Mouchiroud D, Duret L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet. 2005;14(3):421\u20137.","journal-title":"Human Molecular Genetics"},{"key":"2440_CR32","doi-asserted-by":"publisher","unstructured":"Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes. \n                    https:\/\/doi.org\/10.1101\/270157\n                    \n                  .","DOI":"10.1101\/270157"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2440-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2440-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2440-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,19]],"date-time":"2019-11-19T00:05:15Z","timestamp":1574121915000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2440-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,19]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2440"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2440-7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,19]]},"assertion":[{"value":"1 August 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 October 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"N\/A.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"429"}}