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agladstein edited this page Jan 23, 2018 · 7 revisions

SimPrily

Created by Ariella Gladstein, based on code from Consuelo Quinto Cortes and Krishna Veeramah. Also worked on by David Christy, Logan Gantner, and Mack Skodiak.
agladstein@email.arizona.edu

About

SimPrily runs genome simulations with user defined parameters or parameters randomly generated by priors and computes genomic statistics on the simulation output.
Version 1

  1. Run genome simulation with model defined by prior distributions of parameters and demographic model structure.
  2. Take into account SNP array ascertainment bias by creating pseudo array based on priors of number of samples of discovery populations and allele frequency cut-off.
  3. Calculate genomic summary statistics on simulated genomes and pseudo arrays.

This is ideal for use with Approximate Bayesian Computation on whole genome or SNP array data.

Uses c++ programs macs and GERMLINE. For more information on these programs, see:
https://github.com/gchen98/macs
https://github.com/sgusev/GERMLINE

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