GSR: Simulator - sim1000G
Attribute | Value |
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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 | 6 years ago |
Homepage | https://github.com/adimitromanolakis/sim1000G |
Citations | Dimitromanolakis A, Xu J, Krol A, Briollais L, sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs., BMC Bioinformatics, 01-15-2019 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 01-18-2023 (429 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 |
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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 | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used sim1000G.
2022
Zhou D, Gamazon ER, Integrative transcriptomic, evolutionary, and causal inference framework for region-level analysis: Application to COVID-19., NPJ Genom Med, 03-22-2022 [Abstract]
2021
Choi YH, Briollais L, He W, Kopciuk K, FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs., J Stat Softw, 03-01-2021 [Abstract]
2020
Gleason KJ, Yang F, Pierce BL, He X, Chen LS, Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits., Genome Biol, 09-11-2020 [Abstract]