{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:39:00Z","timestamp":1740184740336,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T00:00:00Z","timestamp":1576108800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["01ZX1601F","031L0030A","01ZZ1804D"],"award-info":[{"award-number":["01ZX1601F","031L0030A","01ZZ1804D"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer diagnosis and therapy. While solutions for the large-scale analysis of somatic variants have been implemented, existing solutions often have issues with reproducibility, scalability and interoperability.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Clinical Variant Annotation Pipeline (ClinVAP) is an automated pipeline which annotates, filters and prioritizes somatic single nucleotide variants provided in variant call format. It augments the variant information with documented or predicted clinical effect. These annotated variants are prioritized based on driver gene status and druggability. ClinVAP is available as a fully containerized, self-contained pipeline maximizing reproducibility and scalability allowing the analysis of larger scale data. The resulting JSON-based report is suited for automated downstream processing, but ClinVAP can also automatically render the information into a user-defined template to yield a human-readable report.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ClinVAP is available at https:\/\/github.com\/PersonalizedOncology\/ClinVAP.<\/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\/btz924","type":"journal-article","created":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T12:08:41Z","timestamp":1575893321000},"page":"2316-2317","source":"Crossref","is-referenced-by-count":4,"title":["ClinVAP: a reporting strategy from variants to therapeutic options"],"prefix":"10.1093","volume":"36","author":[{"given":"Bilge","family":"S\u00fcr\u00fcn","sequence":"first","affiliation":[{"name":"Department of Computer Science, Applied Bioinformatics , T\u00fcbingen 72076, Germany"}]},{"given":"Charlotta P I","family":"Sch\u00e4rfe","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Applied Bioinformatics , T\u00fcbingen 72076, Germany"}]},{"given":"Mathew R","family":"Divine","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Applied Bioinformatics , T\u00fcbingen 72076, Germany"}]},{"given":"Julian","family":"Heinrich","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Applied Bioinformatics , T\u00fcbingen 72076, Germany"}]},{"given":"Nora C","family":"Toussaint","sequence":"additional","affiliation":[{"name":"NEXUS Personalized Health Technologies, ETH Zurich , Zurich 8093, Switzerland"}]},{"given":"Lukas","family":"Zimmermann","sequence":"additional","affiliation":[{"name":"Translational Bioinformatics, University Hospital T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"given":"Janina","family":"Beha","sequence":"additional","affiliation":[{"name":"Center for Personalized Medicine, University Hospital T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1739-4598","authenticated-orcid":false,"given":"Oliver","family":"Kohlbacher","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Applied Bioinformatics , T\u00fcbingen 72076, Germany"},{"name":"Center for Personalized Medicine, University Hospital T\u00fcbingen , T\u00fcbingen 72076, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,12,12]]},"reference":[{"key":"2023062300073322900_btz924-B1","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. 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