GSR: Simulator - SomatoSim

Basic Package Attributes
AttributeValue
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, 3 months ago
Homepagehttps://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 CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluatedDec. 9, 2022 (862 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
VariationsSingle Nucleotide Variation,
Simulation Method
Input
Data Type
File formatSAM or BAM,
Output
Data Type
Sequencing Reads
File FormatSAM 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
InterfaceCommand-line,
Development
Tested Platforms
LanguagePython,
License
GSR CertificationAccessibility, 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]


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