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Compiling:

Note: MersenneTwister.h needs to be in the same folder as .c source file. Compile all files using:
g++ <source>.c -o <desired executable name>

• GeneDropping.c - perform genedropping simulations
• GeneDroppingCohorts.c - perform genedropping simulations
• GeneDropping_CarrierBurden.c - perform genedropping simulations, assigning each founder x mutations. Calculate number and proportion of study subjects with a given carrier burden. Calculate number of mutations surviving in the study sample.
• GeneDropping_CarrierBurden_CI.c - perform genedropping simulations, assigning each founder x mutations and provide mean carrier burden among study subjects in each simulation. Use output to calculate 95% confidence interval for mean carrier burden among the individuals from the study sample.
• GeneDropping_FounderContribution.c - perform genedropping simulations and calculate % of variants attribuate to a given founder

Input file formats:

• config file - file with paths/names of all input files as well as "fitness" of mutations
• pedigree file - tab-delimited
  • subject \t mother \t father
  • founders listed first with 0 as IDs of mother and father
  • sorted so all parents come before children
• cohort file - tab-delimited
  • subject \t cohortnum
  • used to either define which individuals are in study sample (cohortnum=1, all others cohortnum=0)
  • or used to sort individuals into birth cohorts (cohortnums 0, 1, 2, ...)