isma

isma integrates somatic mutation calls from multiple mutation-calling pipelines to produce a consensus mutation catalogue that improves reliability of somatic mutation detection in matched tumor–normal next-generation sequencing data.

Key Features:

• R package: Implemented in R and provides functions for integration and analysis of somatic mutation calls.
• Integration of multiple pipelines: Combines somatic mutation outputs from various callers applied to matched tumor–normal samples to address low concordance among tools.
• Quantification of concordance and variability: Computes agreement metrics between pipelines, estimates variability in mutation calls, and identifies outlier results.
• Integration with public mutation catalogues: Incorporates evidence from public resources such as The Cancer Genome Atlas (TCGA) to contextualize mutations.
• Filtering strategies: Provides functions to apply filtering criteria and reports common patterns and pipeline-specific variability to prioritize reliable mutation sites.
• Comprehensive reporting: Generates a unique mutation catalogue and detailed reports summarizing shared patterns, variability, and previously catalogued sites.

Scientific Applications:

• Cancer genomics: Supports accurate somatic mutation detection and comparative analysis across pipelines to aid interpretation of tumor genetic alterations and development of targeted therapies.

Methodology:

Integrates outputs from multiple mutation-calling pipelines applied to matched tumor–normal samples, quantifies agreement between pipelines, estimates variability, identifies outliers, incorporates TCGA evidence, applies filtering strategies, and generates a unique mutation catalogue with detailed reports.