{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T16:46:50Z","timestamp":1762015610449,"version":"3.37.3"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,26]],"date-time":"2018-06-26T00:00:00Z","timestamp":1529971200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Triage-MDS"},{"name":"ERA-Net TRANSCAN BMBF","award":["01KT1401"],"award-info":[{"award-number":["01KT1401"]}]},{"name":"-Horizon2020 MDS-RIGHT","award":["634789"],"award-info":[{"award-number":["634789"]}]},{"DOI":"10.13039\/501100005972","name":"Deutsche Krebshilfe","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Verbesserung der Diagnostik von Tumorerkrankungen durch neue DNA-Sequenzierverfahren und Algorithmen","award":["110495"],"award-info":[{"award-number":["110495"]}]},{"name":"Swedish Cancer Society to Eva Hellstr\u00f6m-Lindberg"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The application of next-generation sequencing in research and particularly in clinical routine requires valid variant calling results. However, evaluation of several commonly used tools has pointed out that not a single tool meets this requirement. False positive as well as false negative calls necessitate additional experiments and extensive manual work. Intelligent combination and output filtration of different tools could significantly improve the current situation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed appreci8, an automatic variant calling pipeline for calling single nucleotide variants and short indels by combining and filtering the output of eight open-source variant calling tools, based on a novel artifact- and polymorphism score. Appreci8 was trained on two data sets from patients with myelodysplastic syndrome, covering 165 Illumina samples. Subsequently, appreci8\u2019s performance was tested on five independent data sets, covering 513 samples. Variation in sequencing platform, target region and disease entity was considered. All calls were validated by re-sequencing on the same platform, a different platform or expert-based review. Sensitivity of appreci8 ranged between 0.93 and 1.00, while positive predictive value ranged between 0.65 and 1.00. In all cases, appreci8 showed superior performance compared to any evaluated alternative approach.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Appreci8 is freely available at https:\/\/hub.docker.com\/r\/wwuimi\/appreci8\/. Sequencing data (BAM files) of the 678 patients analyzed with appreci8 have been deposited into the NCBI Sequence Read Archive (BioProjectID: 388411; https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA388411).<\/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\/bty518","type":"journal-article","created":{"date-parts":[[2018,6,25]],"date-time":"2018-06-25T19:14:47Z","timestamp":1529954087000},"page":"4205-4212","source":"Crossref","is-referenced-by-count":29,"title":["appreci8: a pipeline for precise variant calling integrating 8 tools"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5011-0641","authenticated-orcid":false,"given":"Sarah","family":"Sandmann","sequence":"first","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]},{"given":"Mohsen","family":"Karimi","sequence":"additional","affiliation":[{"name":"Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Aniek O","family":"de Graaf","sequence":"additional","affiliation":[{"name":"Laboratory Hematology, RadboudUMC, Nijmegen GA, The Netherlands"}]},{"given":"Christian","family":"Rohde","sequence":"additional","affiliation":[{"name":"Department of Hematology, Oncology, and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany"}]},{"given":"Stefanie","family":"G\u00f6llner","sequence":"additional","affiliation":[{"name":"Department of Hematology, Oncology, and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany"}]},{"given":"Julian","family":"Varghese","sequence":"additional","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]},{"given":"Jan","family":"Ernsting","sequence":"additional","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]},{"given":"Gunilla","family":"Walldin","sequence":"additional","affiliation":[{"name":"Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Bert A","family":"van der Reijden","sequence":"additional","affiliation":[{"name":"Laboratory Hematology, RadboudUMC, Nijmegen GA, The Netherlands"}]},{"given":"Carsten","family":"M\u00fcller-Tidow","sequence":"additional","affiliation":[{"name":"Department of Hematology, Oncology, and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany"}]},{"given":"Luca","family":"Malcovati","sequence":"additional","affiliation":[{"name":"Departments of Hematology Oncology & Molecular Medicine, Fondazione IRCCS Policlinico San Matteo & University of Pavia, Pavia, Italy"}]},{"given":"Eva","family":"Hellstr\u00f6m-Lindberg","sequence":"additional","affiliation":[{"name":"Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Joop H","family":"Jansen","sequence":"additional","affiliation":[{"name":"Laboratory Hematology, RadboudUMC, Nijmegen GA, The Netherlands"}]},{"given":"Martin","family":"Dugas","sequence":"additional","affiliation":[{"name":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,6,26]]},"reference":[{"key":"2023012712250718300_bty518-B1","doi-asserted-by":"crossref","first-page":"baw093","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database (Oxford)"},{"key":"2023012712250718300_bty518-B2","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nrg.2016.86","article-title":"Towards precision medicine","volume":"17","author":"Ashley","year":"2016","journal-title":"Nat. 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