Post date: Sep 21, 2018 9:56:27 PM
pwd: /uufs/chpc.utah.edu/common/home/u0795641/projects/cmac_qtl/structure
1. sbatch structure.sh
This shell script submits RunStructureFork.pl, which opens and reads jobs.txt line by line, submitting each job in parallel. For each line (3), 5 chains of structure are run using the extraparams option of STARTATPOPINFO 0 or STARTATPOPINFO 1
2. Two files will be output for each chain: Lx_struc_out(_popinfo).txt_f and Lx_struc_out(_popinfo).txt_ss, which give summaries and site-by-site posterior probabilities of ancestry, respectively.
For site-by-site files, columns represent: individual, locus, pp of AA (Lentil/Lentil), AB, BA, and BB (Mung/Mung). We would expect that generally AA=0.75 and AB=0.25 since the backcross consists of AAxAB. The difference between STARTATPOPINFO 0/1 was negligible, so use either.