Article
Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection.
Current protocols in bioinformatics - 1 Dec 2013
Koboldt Daniel C, Larson David E, Wilson Richard K
Abstract excerpt
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)...
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