CaMutQC

CaMutQC performs integrative quality control and filtration of cancer somatic mutations to remove false positives, select candidate mutations, and estimate Tumor Mutation Burden.

Key Features:

• False Positive Removal: Eliminates false positive mutations resulting from technical bias using heuristic quality control and soft-filtering approaches.
• Mutation Candidate Selection: Selects potential mutation candidates for downstream cancer genomics analysis.
• Tumor Mutation Burden Estimation: Estimates Tumor Mutation Burden as part of the integrated filtration workflow.
• Union Strategy: Rescues additional true positive mutations through an embedded union strategy.
• Filter Report and Code Log: Generates a detailed filter report and code log to assist with recording and comparison of filtration parameters.
• Customizable Parameters: Supports both default and customized filtering parameters in a single line of code.

Scientific Applications:

• Cancer Genomics Quality Control: Standardizes quality control and filtration of cancer somatic mutations to improve efficiency, accuracy, and comparability across studies.
• Whole-exome Sequencing Analysis: Applied to WES benchmark datasets to eliminate false positive mutations while retaining true positive mutations.
• Tumor Mutation Burden Profiling: Enables estimation of Tumor Mutation Burden for downstream cancer research applications.

Methodology:

CaMutQC employs heuristic quality control and soft-filtering methods executed through an R/Bioconductor package framework, with default or customized parameters applied in a single line of code.