Post date: May 29, 2015 10:8:37 PM
I decided to run another set of tests with the selection simulations to see how changing the number of SNPs in the window for local ancestry calculations affects ancestry frequency inference (perhaps this will make it easier to infer extreme ancestries). So, I changed -n from 4 to 10 (i.e. 10 SNPs on each side of a focal SNP) and re-ran the analyses. Here is the an example command:
cd /local/scratch/
sleep 5
popanc -o estpanc_n10weakselGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 10 -d 10 -s 1 -c 1.3 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/selection/genoP0F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoP1F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoAdmixF_r9gen_weaksel_gens50.txt
scp estpanc_n10weakselGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/