CaMutQC

CaMutQC filters false positive cancer somatic mutations arising from technical bias and selects candidate cancer mutations by labeling variants with quality flags for downstream cancer genomics analysis.

Key Features:

• False Positive Filtration: Removes false positive mutations generated due to technical issues through heuristic quality control and soft-filtering functions.
• Candidate Mutation Selection: Selects potential cancer mutation candidates by labeling mutations with various flags through well-structured functions.
• Tumor Mutational Burden Estimation: Integrates several methods and gene panels for Tumor Mutational Burden (TMB) estimation.
• Reproducibility Support: Generates a filter report and code log after the filtration process to facilitate reproducibility and comparison.

Scientific Applications:

• Cancer Somatic Mutation Quality Control: Provides standardized filtering criteria for cancer somatic mutations to improve efficiency, accuracy, and reproducibility across studies.
• Whole-exome Sequencing Analysis: Demonstrated capability to eliminate 85.55% of false positive Single Nucleotide Variants (SNVs) while retaining 90.72% of true positive SNVs, with an additional 11.56% of true positive SNVs rescued through a built-in union strategy, with similar results for Insertions and Deletions (INDELs).

Methodology:

Heuristic quality control and soft-filtering approach using default or customized parameters with a built-in union strategy for rescuing true positive variants.