Simulation Program Detail¶
- AlleleFreqTopSim
The Mendelian gene drop, choosing AlleleFreqTopSim selects alleles to be dropped from the founders in the pedigree structure.
- HapFreqTopSim
For the Mendelian gene drop, selecting HapFreqTopSim drops haplotypes from the founders in the pedigrees.
- HapMCTopTogether
This program uses Alun Thomas’s GCHap to find maxiumn likelihood estimates of the haplotypes and their frequencies from genotyped CASE and CONTROL individuals. We uses these estimated haplotypes and their frequencies for the gene-drop. Then all individual’s haplotype data will be phased before testing.
- HapMCTopSeparate
This program is similar to HapMCTopTogether, except we separate individuals into CASE and CONTROL and uses GCHap to estimate each group’s haplotypes and their frequencies. Finally, we phased the two groups of data separately.
- GeneCounterTopSim
The Mendelian gene drop, using Alun Thomas’s GeneCountAlleles program to calculate allele frequencies based on all the genotyped members and the population allele frequencies in the linkage loci data file.
- IndivWtTopSim
Assigns two unique alleles to all founders and uses a Mendelian gene drop to assign these to the rest of the pedigree for use in weighting algorithm.
- ConditionalGeneTopSim
This program uses Alun Thomas’sConditionalGeneDrop program to preform the gene drop