GSR: Simulator - sim1000G

Basic Package Attributes
AttributeValue
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
Homepagehttps://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 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 DataGenotype at Genetic Markers,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodOther,
Input
Data TypeOther,
File formatOther,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File Format
Sample TypeRandom 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
RecombinationUniform, Varying Recombination Rates,
Mutation Models
Events Allowed
Other
InterfaceScript-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageR,
LicenseGNU Public License,
GSR Certification

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