After I ran entropy, I needed to create genotype likelihood files to do further analysis with popanc. To do this I used est_popmod.
Here is the command I used:
/uufs/chpc.utah.edu/common/home/u6000989/bin/estpost_entropy -o g_K2.txt -p gprob -s 0 -w 0 ento_lyc_hybridsCh*K2.hdf5
This will convert hdf5 files from each chain to a combined genotype estimate file. This should be repeated for each K = 2,3,4,5. Finally, I ended up with one genotype estimate file per K (4 files, geno_K*.txt).
I used these gene_*.txt files to take averages across all K's for genotype estimates. I did this in R. I then used this average genotype estimates file to plot a PCA. Here is the folder where all the PCA's are saved:
/uufs/chpc.utah.edu/common/home/u6007910/projects/lyc_dubois/entropy/complete/mcmc
For popanc, I needed to split the average genotype estimates file into a file for each population (N = 23). This is because for popanc I will use a ideas file, a Melissa file and then a admixed file. Basically, this the two parents and then the admixed population from those two parents. All these files are in this directory:
/uufs/chpc.utah.edu/common/home/u6007910/projects/lyc_dubois/popanc/infiles.
popanc zg notes: https://sites.google.com/site/gompertlabnotes/home/researcher-pages/zach-gompert/lycaeides/lycaeides-genome-admixture/initialpopancanalyseswithz23chromosome