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. 2013 Dec:44:15.4.1-17.
doi: 10.1002/0471250953.bi1504s44.

Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection

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

Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection

Daniel C Koboldt et al. Curr Protoc Bioinformatics. 2013 Dec.

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.

Keywords: indels; mutation detection; next-generation sequencing; snvs; trio calling; variant calling; varscan 2.

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Figures

Figure 1
Figure 1. VarScan variant calling applications by data type
VarScan identifies single nucleotide both variants (SNVs) and insertion/deletion variants (indels) using the SAMtools mpileup output from one or more BAM files.
See this image and copyright information in PMC

References

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