Pipeline for ABC simulations of multilocus balancing selection and introgression
- Run
bash init.sh
to setup the directory stucture - Run
qsub scripts/pipeline_introgression.sh
to get the simulations for introgression
Note: make sure SLiM is available on your path. You can install it via the following:
# This script is for SLiM 3.2.1. Might not work for newer version of SLiM.
qrsh -l h_data=8G
cd ~
rm SLiM.zip
#download SLiM
wget http://benhaller.com/slim/SLiM.zip
unzip SLiM.zip
#make build directory
mkdir slim_build
cd slim_build
#load newer version of gcc
module load gcc/4.9.3
#tell cmake which one to use and compile
CC=gcc CXX=g++ cmake ../SLiM
make slim
4N until MRCA of all S .cerevisae.
Ne = 10,000,000
migration rate - m uniform(0,1)
talpha = uniform(0,40,000,000)
Selfing rate = 1/50,000 (Kruglyak NG)
Clonning rate = 1/50,000 (use instead of selfing rate)
Gene conversion rate = (this is probably what yeast uses for the most part)
Recombination rate = 3.133483e-06 (BYxRM linkage mapping)
mutation rate = 3.8e-10
number of generations = 3.2 billion.
To set the generation time as a variable, see here: https://groups.google.com/forum/#!topic/slim-discuss/0jOCti_t380
Use -t
and -m
to benchmark time and memory from the command line.