Post date: Jun 01, 2016 7:44:48 PM
Having assigned SNPs to LGs, I am re-running entropy with common and not rare variants. I am excluding the Z chromosome (23).
I used the script addLgInfo.pl to prepend LG and cM information to the following gl files (see below) and sorted the SNPs by LG and cM position. I then dropped chromosome 23. Numbers of SNPs for each data file are given in the table below.
Variant (gl) files are in /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/variants/.
Next, I ran entropy to get at overall admixture proportions with the 22 autosomes and common or not rare SNPs. I considered K = 2-8, 3 chains each. An example is here:
#!/bin/bash
module load gsl
module load hdf5
K=$(($1+2))
/uufs/chpc.utah.edu/common/home/u6000989/bin/entropy -i /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/variants/nosex_lychybanc_common.gl -l 15000 -b 5000 -t 5 -k $K -Q 0 -s 50 -q /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/entropy/startingvals/ldak$K.txt -o /scratch/general/lustre/ento_lhaCommonCh0K$K.hdf5 -w 0 -m 1
mv /scratch/general/lustre/ento_lhaCommonCh0K$K.hdf5 /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/entropy
All results are in /uufs/chpc.utah.edu/common/home/u6000989/projects/lyc_hybanc/entropy/.