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- Title
Combining calls from multiple somatic mutation-callers.
- Authors
Kim, Su Yeon; Jacob, Laurent; Speed, Terence P.
- 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, mutationcalling 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.
- Subjects
SOMATIC mutation; CANCER research; GENETIC databases; ENDOMETRIUM; BIOINFORMATICS
- Publication
BMC Bioinformatics, 2014, Vol 15, Issue 1, p1
- ISSN
1471-2105
- Publication type
Article
- DOI
10.1186/1471-2105-15-154