UNIT 15.4 Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection

  1. Daniel C. Koboldt,
  2. David E. Larson,
  3. Richard K. Wilson

Published Online: 12 DEC 2013

DOI: 10.1002/0471250953.bi1504s44

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Koboldt, D. C., Larson, D. E. and Wilson, R. K. 2013. Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection. Current Protocols in Bioinformatics. 15:15.4:15.4.1–15.4.17.

Author Information

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

Publication History

  1. Published Online: 12 DEC 2013


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. Curr. Protoc. Bioinform. 44:15.4.1-15.4.17. © 2013 by John Wiley & Sons, Inc.


  • variant calling;
  • mutation detection;
  • trio calling;
  • snvs;
  • indels;
  • varscan 2;
  • next-generation sequencing