SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.
Sci Rep. 2020 Jul 30;10(1):12898
Authors: Wang M, Luo W, Jones K, Bian X, Williams R, Higson H, Wu D, Hicks B, Yeager M, Zhu B
It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.
PMID: 32732891 [PubMed – in process]