GSR: Simulator - sim1000G
| Attribute | Value |
|---|---|
| Title | sim1000G |
| Short Description | sim1000G integrates fully with R and can simulate existing variation from a single VCF file. In addition it can also simulate arbitrary pedigrees. |
| Long Description | We develop a new user-friendly and integrated R package, sim1000G, which simulates genomic regions for unrelated individuals or for families. Only a single input of raw phased Variant Call Format (VCF) file is needed. Haplotypes are extracted to compute linkage disequilibrium in the simulated region and then for the generation of new genotype data for unrelated individuals. The covariance across variants is used to preserve the LD structure of the original population. Arbitrary pedigree sizes are generated by modeling recombination events within sim1000G. Various simulation scenarios are presented assuming unrelated individuals from a single population or two distinct populations, or alternatively for three-generation family data. Sim1000G can capture allele frequency diversity, short and long-range linkage disequilibrium (LD) patterns and subtle population differences in LD structure without the need for any tuning parameters. |
| Keywords | simulator variants VCF pedigree |
| Version | 1.19 |
| Project Started | 2018 |
| Last Release | 2 years, 7 months ago |
| Homepage | https://cran.r-project.org/web/packages/sim1000G/index.html |
| Citations | |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Other, |
| Input | |
| Data Type | Other, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | R, |
| License | GNU Public License, |
| GSR Certification |
No example publication using sim1000G has been provided.
Please propose new citations if you are aware of publications that use this software.