{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:51Z","timestamp":1772138091732,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T00:00:00Z","timestamp":1539043200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013114","name":"Broad Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013114","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Next-generation sequencing technology is transitioning quickly from research labs to clinical settings. The diagnosis and treatment selection for many acquired and autosomal conditions necessitate a method for accurately detecting somatic and germline variants.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed Pisces, a rapid, versatile and accurate small-variant calling suite designed for somatic and germline amplicon sequencing applications. Accuracy is achieved by four distinct modules, each incorporating a number of novel algorithmic strategies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Pisces is distributed under an open source license and can be downloaded from https:\/\/github.com\/Illumina\/Pisces. Pisces is available on the BaseSpace\u2122 SequenceHub. It is distributed on Illumina sequencing platforms such as the MiSeq\u2122 and is included in the Praxis\u2122 Extended RAS Panel test which was recently approved by the FDA.<\/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\/bty849","type":"journal-article","created":{"date-parts":[[2018,10,8]],"date-time":"2018-10-08T16:17:06Z","timestamp":1539015426000},"page":"1579-1581","source":"Crossref","is-referenced-by-count":72,"title":["Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data"],"prefix":"10.1093","volume":"35","author":[{"given":"Tamsen","family":"Dunn","sequence":"first","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Gwenn","family":"Berry","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Dorothea","family":"Emig-Agius","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Yu","family":"Jiang","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Serena","family":"Lei","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Anita","family":"Iyer","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Nitin","family":"Udar","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Han-Yu","family":"Chuang","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Jeff","family":"Hegarty","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Michael","family":"Dickover","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Brandy","family":"Klotzle","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Justin","family":"Robbins","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Marina","family":"Bibikova","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]},{"given":"Marc","family":"Peeters","sequence":"additional","affiliation":[{"name":"Department of Oncology, Antwerp University Hospital, Edegem, Belgium"}]},{"given":"Michael","family":"Str\u00f6mberg","sequence":"additional","affiliation":[{"name":"Departments of Bioinformatics and Clinical Genomics, Illumina Inc., San Diego, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,10,9]]},"reference":[{"key":"2023012806492569900_bty849-B1","doi-asserted-by":"crossref","first-page":"e0127146.","DOI":"10.1371\/journal.pone.0127146","article-title":"Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples","volume":"10","author":"Betge","year":"2015","journal-title":"PLoS One"},{"key":"2023012806492569900_bty849-B2","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/cgt.2015.39","article-title":"A 2015 update on predictive molecular pathology and its role in targeted cancer therapy: a review focusing on clinical relevance","volume":"22","author":"Dietel","year":"2015","journal-title":"Cancer Gene Ther"},{"key":"2023012806492569900_bty849-B3","doi-asserted-by":"crossref","first-page":"253","DOI":"10.2174\/1389202915666150511205313","article-title":"Clinical next generation sequencing for precision medicine in cancer","volume":"16","author":"Dong","year":"2015","journal-title":"Curr. 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