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Journal Articles BMC Bioinformatics Year : 2014

Combining calls from multiple somatic mutation-callers

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S. Y. Kim
  • Function : Author
T. P. Speed
  • Function : Author

Abstract

Background: Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperforms all others. Therefore, fully utilizing multiple callers can be a powerful way to construct a list of final calls for one's research. Results: Using a set of mutations from multiple callers that are impartially validated, we present a statistical approach for building a combined caller, which can be applied to combine calls in a wider dataset generated using a similar protocol. Using the mutation outputs and the validation data from The Cancer Genome Atlas endometrial study (6,746 sites), we demonstrate how to build a statistical model that predicts the probability of each call being a somatic mutation, based on the detection status of multiple callers and a few associated features. Conclusion: The approach allows us to build a combined caller across the full range of stringency levels, which outperforms all of the individual callers.

Dates and versions

hal-02046830 , version 1 (22-02-2019)

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S. Y. Kim, Laurent Jacob, T. P. Speed. Combining calls from multiple somatic mutation-callers. BMC Bioinformatics, 2014, 15, pp.154. ⟨10.1186/1471-2105-15-154⟩. ⟨hal-02046830⟩
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