title: Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection.
abstract: The identification of small sequence variants remains a challenging but critical step in the analysis of next-generation sequencing data. Our variant calling tool, VarScan 2, employs heuristic and statistic thresholds based on user-defined criteria to call variants using SAMtools mpileup data as input. Here, we provide guidelines for generating that input, and describe protocols for using VarScan 2 to (1) identify germline variants in individual samples; (2) call somatic mutations, copy number alterations, and LOH events in tumor-normal pairs; and (3) identify germline variants, de novo mutations, and Mendelian inheritance errors in family trios. Further, we describe a strategy for variant filtering that removes likely false positives associated with common sequencing- and alignment-related artifacts.
authors.affiliation: The Genome Institute at Washington University in St. Louis, Missouri 63108, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Koboldt
authors.affiliation: The Genome Institute at Washington University in St. Louis, Missouri, USA, 63108.
authors.forename: David E
authors.initials: DE
authors.lastname: Larson
authors.affiliation: The Genome Institute at Washington University in St. Louis, Missouri, USA, 63108.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
mesh_terms: D016678:Genome; D005854:Germ Cells / Q000378:metabolism*; D006801:Humans; D009154:Mutation / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software
keywords: indels; mutation detection; next-generation sequencing; snvs; trio calling; variant calling; varscan 2