Use Cases¶
Is SimPrily right for your research?
| Use case | Can SimPrily be used? | Notes | |
|---|---|---|---|
| Type of simulation | Coalescent simulation | yes | |
| Forward simulation | no | ||
| Model | Selection | no | |
| Demographic model | yes | See MaCS/ms documentation | |
| Recombination map | yes | Not necessary, but sims will be more accurate | |
| Constant mutation rate | yes | ||
| Constant model parameters | yes | ||
| Uniform priors of parameters | yes | ||
| Non-uniform priors | no | ||
| Known SNP ascertainment | yes | ||
| Unknown SNP ascertainment | yes | See Quinto-Cortes et al. (2018) | |
| Size of simulation | Chromosome-size loci | yes | |
| Whole genome | no | Must simulate each chromosome separately | |
| 1000’s of samples | no | Try msprime | |
| Type of simulated data | Sequence (variant) data | yes | |
| Exome data | yes | ||
| SNP array data | yes | ||
| Microsatellite/str data | no | ||
| Returned data | AFS Summary statistics | yes | |
| IBD Summary statistics | yes | Only with SNP array option | |
| Raw simulated output | no | ||
| PLINK ped/map output | yes | Only with SNP array option | |
| Programing experience | None | yes | Use the Discovery Environment app |
| Beginner command line | yes | Can use the Open Science Grid | |
| Python | yes | Not necessary, but can add own functions and make pull requests |
If you still are not sure if SimPrily is right for your research check out other simulators at https://popmodels.cancercontrol.cancer.gov/gsr