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SomatoSim: precision simulation of somatic single nucleotide variants
Marwan A Hawari1, Celine S Hong2, Leslie G Biesecker1
1Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
BMC Bioinformatics
|March 7, 2021
Summary
SomatoSim is a new, user-friendly tool for simulating somatic single nucleotide variants in sequencing data. It offers high customizability for precise variant calling performance analysis.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Somatic single nucleotide variants are crucial in cancer development.
- High-throughput sequencing necessitates accurate variant identification tools.
- Simulated data is vital for benchmarking somatic variant callers due to the lack of gold standards.
Purpose of the Study:
- To introduce SomatoSim, a novel tool for simulating somatic single nucleotide variants.
- To provide a highly customizable platform for understanding variant calling performance.
Main Methods:
- SomatoSim simulates somatic single nucleotide variants within existing Sequence Alignment Map (SAM/BAM) files.
- The process involves three stages: variant selection, simulation, and evaluation.
- Users can control variant positions, allele fractions, coverage, and quality metrics.
Main Results:
- SomatoSim enables precise simulation of somatic single nucleotide variants.
- The tool offers detailed control over simulation parameters.
- It facilitates focused analysis of single nucleotide variant calling performance.
Conclusions:
- SomatoSim is a user-friendly and highly customizable tool for simulating somatic single nucleotide variants.
- It addresses limitations of existing simulation tools by allowing precise control.
- The tool is available for public use.
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