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GSR: Simulator - SomatoSim
| Attribute | Value |
|---|---|
| Title | SomatoSim |
| Short Description | SomatoSim: precision simulation of somatic single nucleotide variants |
| Long Description | SomatoSim is a tool that lets users simulate somatic single nucleotide variants in sequence alignment map (SAM/BAM) files with full control of the specific variant positions, number of variants, variant allele fractions, depth of coverage, read quality, and base quality, among other parameters. SomatoSim accomplishes this through a three-stage process: variant selection, where candidate positions are selected for simulation, variant simulation, where reads are selected and mutated, and variant evaluation, where SomatoSim summarizes the simulation results. |
| Keywords | Single nucleotide variants, SNV, Simulation, Somatic variants, Mosaicism |
| Version | 1.0.0 |
| Project Started | 2020 |
| Last Release | 5 years, 4 months ago |
| Homepage | https://github.com/BieseckerLab/SomatoSim |
| Citations | Hawari MA, Hong CS, Biesecker LG, SomatoSim: precision simulation of somatic single nucleotide variants., BMC Bioinformatics, March 6, 2021 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Dec. 9, 2022 (986 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | |
| Variations | Single Nucleotide Variation, |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | SAM or BAM, |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | SAM or BAM, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used SomatoSim.
2022
Kwok AWC, Qiao C, Huang R, Sham MH, Ho JWK, Huang Y, MQuad enables clonal substructure discovery using single cell mitochondrial variants., Nat Commun, March 8, 2022 [Abstract]
2021
Dudley JN, Hong CS, Hawari MA, Shwetar J, Sapp JC, Lack J, Shiferaw H, NISC Comparative Sequencing Program., Johnston JJ, Biesecker LG, Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach., BMC Bioinformatics, April 8, 2021 [Abstract]