#run neutral simulations for 10Mbp region for Hcor and Hham using macs and then ran SweeD #for determining significance cutoff for the genome-wide SweeD scan #first parameter is number of haplotypes #second parameter is lenght of region #-t is mutation rate *4Ne #-r is recombination rate *4Ne #Hcor Ne: 1174297 #Hham Ne: 1115822 #mutation rate: 2.8e-9 #recombination rate: 1.12e-8 bsub -o log.txt ./macs.sh bsub -o log.txt "python Hcor_macs_to_vcf.py" bsub -o log.txt "python Hham_macs_to_vcf.py" for file in *_neutral_macs_100haplotypes_rep*.vcf do prefix=${file//.vcf/} bsub -o log.txt -n 8 "SweeD-P -input ${file} -grid 10000 -threads 8 -folded -name ${prefix}" done