Accelerated Somatic Mutation Calling for Whole-Genome and Whole-Exome Sequencing Data From Heterogenous Tumor Samples

Authors

Shuangxi Ji
Tong Zhu
Ankit Sethia
Wenyi Wang

Publication Date

5-15-2024

Journal

Genome Research

Abstract

Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were 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 multistep parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times more than MuSE 1 and eight to 80 times more 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 data sets.

Keywords

Humans, Neoplasms, Mutation, Exome Sequencing, Whole Genome Sequencing, Software, Genome, Human, Genomics, Algorithms, DNA Mutational Analysis

Comments

Associated Data

PMID: 38589250

DOI

10.1101/gr.278456.123

PMID

38589250

PMCID

PMC11146589

PubMedCentral® Posted Date

April 2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes