This repository contains code related to: Diet unmasks genetic variants that regulate lifespan in outbred Drosophila L Pallares*, AJ Lea*, et al. https://www.biorxiv.org/content/10.1101/2020.10.19.346312v2 Specifically, the processing steps that are described here are: 1) Trimming, mapping, and genotyping each sequence data derived from each sample 2) Joint genotyping all samples together (by chromosome) 3) Extracting counts of the number of reads that mapped to the reference and alternate allele for each sample And the analyses that are described here are: 1) Using a beta binomial model to test for allele frequency differences between t0 and tN in each environment 2) Permutations of the factor of interest (t0, tN_HS, tN_CTRL) in the beta binomial model 3) Estimating the allele frequency change between t0 and tN from model coefficents 4) Simulating data to be analyzed using a beta binomial vs CMH approach 5) Testing to see if lifespan associated SNPs followed particular trajectories hypothesized by different theories of aging 6) Testing whether lifespan decreasing alleles are more likely to be derived vs ancestral, relative to frequency matched sites Additional code can be found at: https://github.com/Lufpa/Longevity Data files pointed to in these scripts (as well as additional summary files) are available on Dryad: doi:10.5061/dryad.hhmgqnkgr. Note that the specific paths in the scripts will not work on your computer and you will need to change them accordingly. Please contact me at amandalea7180@gmail.com with any questions.