ClonalSim

ClonalSim generates realistic mutational profiles of tumor samples with hierarchical clonal structure for benchmarking variant callers, testing clonal deconvolution algorithms, and teaching tumor heterogeneity concepts.

Key Features:

• Clonal mutation simulation: Simulates founder, shared, and private mutations within hierarchical clonal structures.
• Intra-tumor heterogeneity modeling: Incorporates biological noise through Beta distribution.
• Technical sequencing noise modeling: Implements negative binomial depth variation, binomial read sampling, and base errors.

Scientific Applications:

• Variant caller benchmarking: Provides realistic simulated data for evaluating variant calling algorithms.
• Clonal deconvolution testing: Enables assessment of algorithms that infer clonal composition from sequencing data.
• Educational use: Supports teaching of tumor heterogeneity concepts through controlled simulation scenarios.

Methodology:

ClonalSim simulates mutational profiles using biologically realistic noise models including intra-tumor heterogeneity via Beta distribution and technical sequencing noise via negative binomial depth variation, binomial read sampling, and base errors.