{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:52Z","timestamp":1753875772286,"version":"3.41.2"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,5,21]],"date-time":"2020-05-21T00:00:00Z","timestamp":1590019200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of Education, Universities and Research","award":["PRIN #2017PPS2X4_003"],"award-info":[{"award-number":["PRIN #2017PPS2X4_003"]}]},{"DOI":"10.13039\/501100005010","name":"Italian Association for Cancer Research","doi-asserted-by":"publisher","award":["MFAG #15674","IG #20216","IG #20052"],"award-info":[{"award-number":["MFAG #15674","IG #20216","IG #20052"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Whole exome sequencing (WES) is a powerful approach for discovering sequence variants in cancer cells but its time effectiveness is limited by the complexity and issues of WES data analysis. Here we present iWhale, a customizable pipeline based on Docker and SCons, reliably detecting somatic variants by three complementary callers (MuTect2, Strelka2 and VarScan2). The results are combined to obtain a single variant call format file for each sample and variants are annotated by integrating a wide range of information extracted from several reference databases, ultimately allowing variant and gene prioritization according to different criteria. iWhale allows users to conduct a complex series of WES analyses with a powerful yet customizable and easy-to-use tool, running on most operating systems (macOs, GNU\/Linux and Windows).<\/jats:p>\n               <jats:p>iWhale code is freely available at https:\/\/github.com\/alexcoppe\/iWhale and the docker image is downloadable from https:\/\/hub.docker.com\/r\/alexcoppe\/iwhale.<\/jats:p>","DOI":"10.1093\/bib\/bbaa065","type":"journal-article","created":{"date-parts":[[2020,3,30]],"date-time":"2020-03-30T19:14:23Z","timestamp":1585595663000},"source":"Crossref","is-referenced-by-count":10,"title":["iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data"],"prefix":"10.1093","volume":"22","author":[{"given":"Andrea","family":"Binatti","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Bresolin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefania","family":"Bortoluzzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Coppe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,20]]},"reference":[{"key":"2021103114492688900_ref1","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1126\/science.1235122","article-title":"Cancer genome 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