sidavad / ancestryinference Goto Github PK

This folder contains all the code for simulating admixture ( ~36 simulations ) as well as for inferring admixture proportions in parents using HapMix. We dont do grandparental admixture inference here.

create-Hapmix-files.sh create the input files for HapMix

create-Hapmix-files_all.sh create the HapMix input files for all simulations and for all chromosomes

infer-admix_all.sh Average all the HapMix results for each chromosome and then over all chromosomes for each simulation. Output is the averaged results for each simulation

pickcols.awk pick columns from a large text file according to a second file list

run-Hapmix_all.sh run HapMix over all simulations and chromosomes

scratch.sh scratch file for shell code

selectColumn.awk selectColumns from a file according to hard coded pattern match

simulate-admix-pedigree.sh simulate admixture using ped-sim and then pruning the output

split-admix-pedigree.sh create infer and holdout vcfs from simulate-admix-pedigree output