Code for genomic simulations and Approximate Bayesian Computation for the paper:

Substructured population growth in the Ashkenazi Jews inferred with Approximate Bayesian Computation

Created by Ariella Gladstein
[email protected]

https://doi.org/10.1093/molbev/msz047

Preprint available at: https://doi.org/10.1101/467761

Documentation

Please go to the wiki!

Data Availability

The final simulation output can be accessed on figshare https://figshare.com/projects/Substructured_population_growth_in_the_Ashkenazi_Jews_inferred_with_Approximate_Bayesian_Computation/37856

• Chromosome 1 simulation summary statistics: https://doi.org/10.6084/m9.figshare.7503854.v1
• Whole genome simulation summary statistics: https://doi.org/10.6084/m9.figshare.7010180.v1
• Chromosomes 2-5 updated posterior as priors simulation summary statistics: https://doi.org/10.6084/m9.figshare.7010195.v1
• Whole genome sequence and SNP array data used to calucate summary statistics for ABC: https://doi.org/10.6084/m9.figshare.7503812.v1
• Original Ashkenazi SNP array data: https://doi.org/10.6084/m9.figshare.7503827.v1
• Ashkenazi SNP array data in PLINK format, hg18: https://doi.org/10.6084/m9.figshare.7503815.v1
• Combined Jewish, European, and Middle Eastern SNP array data: https://doi.org/10.6084/m9.figshare.7503818.v1

Citation

If you make use of this work in your research, we would appreciate the following citation:

Gladstein A.L. and Hammer M.F. (2019). Substructured population growth in the Ashkenazi Jews inferred with Approximate Bayesian Computation. Molecular Biology And Evolution. Molecular Biology and Evolution, msz047. https://doi.org/10.1093/molbev/msz047

@article{10.1093/molbev/msz047,
    author = {Gladstein, Ariella L and Hammer, Michael F},
    title = "{Substructured population growth in the Ashkenazi Jews inferred with Approximate Bayesian Computation}",
    year = {2019},
    month = {03},
    doi = {10.1093/molbev/msz047},
    url = {https://dx.doi.org/10.1093/molbev/msz047},
}

This work is based on code from Consuelo Quinto-Cortes and Krishna Veeramah, used in the papers:

Quinto-Cortés, C. D., Woerner, A. E., Watkins, J. C., & Hammer, M. F. (2018). Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference. Scientific Reports, 8, 10209. http://doi.org/10.1038/s41598-018-28539-y

Veeramah, K. R., Wegmann, D., Woerner, A., Mendez, F. L., Watkins, J. C., Destro-Bisol, G., … Hammer, M. F. (2012). An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data. Molecular Biology and Evolution, 29(2), 617–630. http://doi.org/10.1093/molbev/msr212