Introduction

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.

Publications

  1. Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection.
    Cite this
    Koboldt DC, Larson DE, Wilson RK, 2013-12-01 - Current protocols in bioinformatics
  2. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
    Cite this
    Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK, 2012-03-01 - Genome research
  3. VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
    Cite this
    Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L, 2009-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Daniel C Koboldt
    Developer

    The Genome Institute at Washington University in St. Louis, Missouri 63108, United States of America

  2. David E Larson
    Developer

    The Genome Institute at Washington University in St. Louis, Missouri

  3. Richard K Wilson
    Investigator

    The Genome Institute at Washington University in St. Louis, Missouri

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Summary
AccessionBT000487
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl, R
User InterfaceTerminal Command Line
Download Count0
Submitted ByRichard K Wilson