Rate estimates in VCF format can be downloaded here: http://genetics.bwh.harvard.edu/downloads/Vova/Roulette/
Scripts are provided to facilitate annotating variant data with estimates from Roulette and the two models analyzed as comparison.
Notebooks used to analyze the distribution of allele frequencies (SFS) under recurrent mutation using Roulette estimates.
- Use a demographic model of faster-than-exponential growth to predict the SFS in each Roulette bin.
- Estimate the distribution mutation rates among observed SNVs in RNU, tRNA, and IGK genes.
- Perform simulations to estimate the probability that rare minor alleles are ancestral.
Notebooks used to estimate the residual variance in mutation rates and compare Roulette estimates to other models.
- Calculate pseudo-R^2 for different models and use bootstrap samples to estimate confidence intervals.
- Compare the de novo mutation rates at SNV and non-SNV sites to estimate the residual variance in each mutation rate bin for each model.