Post date: Jan 01, 2015 6:59:19 PM
Here is my plan for the analysis of the initial simulated data sets.
1. Details on simulated data sets:
no of loci = 10010 (1001 per chr. 10 chr, 1 M chromosomes, marker ever 0.1 cM or 1 mM)
pop size = 500
sample size = 50
theta in source pops. = 0.8
Fst between source pops. = 0.3
no of gens. = 10, 100, 1000
Fst between ancest. and sampled admix pops. = exp(-T) * (exp(T) - 1); T = g/N
Fst = 0.0198, 0.181, 0.865
no of reps = 10
2. Cross-validation with scales 0.1, 0.5, 1, 5, 10 (sep. runs for 0.1, 1, 10 = A and 0.5, 5 = B for speed)
one MCMC run each X 30 data sets (10 reps, 3 conditions)
10000 MCMC steps, 5000 burnin, thin 5
estimate Fst
example:
cd /local/scratch/
sleep 0
popanc -o outcv_BF_r9f0.3gen_demog_gens10.hdf5 -m 10000 -b 5000 -t 5 -f 1 -w 0 -v 1 -c 0.5,5 /labs/evolution/projects/popanc_sims/sims/genoP0F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoP1F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoAdmxF_r9f0.3gen_demog_gens10.txt > /labs/evolution/projects/popanc_sims/mcmc/logF_r9f0.3gen_demog_gens10
scp outF_r9f0.3gen_demog_gens10.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
3. Parameter estimatino with scales 0.1, 0.5, 1, 5, 10
two MCMC runs each X 30 data sets (10 reps, 3 conditions) X 5 scale parameters = 300 jobs total
50000 MCMC steps, 10000 burnin, thin 5
estimate Fst
example:
cd /local/scratch/
sleep 5
popanc -o outest_1rep1F_r9f0.3gen_demog_gens10.hdf5 -m 50000 -b 10000 -t 5 -f 1 -w 0 -v 0 -c 1 /labs/evolution/projects/popanc_sims/sims/genoP0F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoP1F_r9f0.3gen_demog_gens10.txt /labs/evolution/projects/popanc_sims/sims/genoAdmxF_r9f0.3gen_demog_gens10.txt > /labs/evolution/projects/popanc_sims/mcmc/log_estest_1rep1F_r9f0.3gen_demog_gens10
scp outest_1rep1F_r9f0.3gen_demog_gens10.hdf5 /labs/evolution/projects/popanc_sims/mcmc/