Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data

• Published in: Bioinformatics (Oxford, England) England), 2019-05, Vol.35 (9), p.1579-1581
• Main Authors: Dunn, Tamsen, Berry, Gwenn, Emig-Agius, Dorothea, Jiang, Yu, Lei, Serena, Iyer, Anita, Udar, Nitin, Chuang, Han-Yu, Hegarty, Jeff, Dickover, Michael, Klotzle, Brandy, Robbins, Justin, Bibikova, Marina, Peeters, Marc, Strömberg, Michael
• Format: Article
• Language: English
• Subjects: Applications Notes; Germ Cells; High-Throughput Nucleotide Sequencing; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/bty849

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. 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. Pisces is distributed under an open source license and can be downloaded from https://github.com/Illumina/Pisces. Pisces is available on the BaseSpace™ SequenceHub. It is distributed on Illumina sequencing platforms such as the MiSeq™ and is included in the Praxis™ Extended RAS Panel test which was recently approved by the FDA. Supplementary data are available at Bioinformatics online.