Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples.

Abstract

Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenge was overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE 2, powered by multi-step parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times than MuSE 1 and 8-80 times than other popular callers. Our benchmark study suggests combining MuSE 2 and the recently accelerated Strelka2 achieves high efficiency and accuracy in analyzing large cancer genomic datasets.