Page Comparison

#change to directory with species-separated vcfs
cd species_separated


#select window size and step (100Kb)
WINDOW_SIZE=100000
WINDOW_STEP=100000


#loop through vcfs and build commands for running --window-pi
>piCommands
for vcfFile in *.recode.vcf
do echo "vcftools --vcf $vcfFile --window-pi $WINDOW_SIZE --window-pi-step $WINDOW_STEP --out ${vcfFile/.recode.vcf} &" >> piCommands
done


#execute them


#look at results files
ls -l *windowed.pi


#send to pungitius_exercise/ on personal computer for plottingto plot with R