Post date: Jan 25, 2015 9:23:11 PM
As I first pass at these data, I am estimating the allele frequencies for each line and generation which I will use to construct a population tree (probably with TreeMix). This will be a nice way to make sure that there are not major problems with these data as the true history of the populations is known.
I am using popmod to estimate the allele frequencies. For each population I am running two chains with 15000 MCMC steps, a burnin of 5000 steps and a thinning interval of 5. The results will end up in /labs/evolution/projects/cmaclentil/popgen/. Here is an example command:
cd /local/scratch/
sleep 5
~/bin/popmod -i /labs/evolution/projects/cmaclentil/variants/cmacpop_M-14.gl -n 15000 -b 5000 -t 4 -o popaf_M-14_chain1.hdf5
scp popaf_M-14_chain1.hdf5 /labs/evolution/projects/cmaclentil/popgen/
rm popaf_M-14_chain1.hdf5