MuSE

Overview

MuSE (Mutation calling using a Markov Substitution model for Evolution) is a somatic SNV caller for tumor/normal paired sequencing data. It models the evolutionary process of cancer cells using a Markov substitution model, enabling context-sensitive variant detection. MuSE showed the highest pair-wise agreement with MuTect among the seven callers in the TCGA MC3 project and detected the largest number of true positive SNVs alongside MuTect.

Used by

One of seven somatic callers in the TCGA MC3 ensemble pipeline run on DNAnexus cloud (~1.8M core-hours) across ~10,510 TCGA tumor/normal pairs from 33 cancer types; showed highest pair-wise agreement with MuTect and highest true-positive SNV detection rate alongside MuTect PMID:29596782

Notes

Performs best for SNV detection; indel calling is handled by other callers (Pindel, Indelocator).
Run on the DNAnexus cloud platform in the MC3 project (not Broad Firehose).
Non-default parameters were required for optimal performance in the MC3 context.

Sources

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