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#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 to plot with R |
Plot results from both sets of analyses A pseudoautosomal region (PAR) is a region of a sex chromosome that still undergoes recombination.
What is the likely boundary for the PAR in Pungitius pungitius? (plot window stats with plot_window_stats.R)
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probably at about 3 Mb |
Fst result
Pi result