Page Comparison

#(back on TACC)
#First choose a window size and step size (here 100Kb)
WINDOW_SIZE=100000
WINDOW_STEP=100000

#Run for chromosome 1
vcftools --vcf chrI.vcf \
 --weir-fst-pop Pun_males.txt \
 --weir-fst-pop Pun_females.txt \
 --fst-window-size $WINDOW_SIZE \
 --fst-window-step $WINDOW_STEP \
 --out chrI_female_v_male

#chromosome 2
vcftools --vcf chrII.vcf \
 --weir-fst-pop Pun_males.txt \
 --weir-fst-pop Pun_females.txt \
 --fst-window-size $WINDOW_SIZE \
 --fst-window-step $WINDOW_STEP \
 --out chrII_female_v_male

#chromosome12
vcftools --vcf chrXII.vcf \
 --weir-fst-pop Pun_males.txt \
 --weir-fst-pop Pun_females.txt \
 --fst-window-size $WINDOW_SIZE \
 --fst-window-step $WINDOW_STEP \
 --out chrXII_female_v_male


#look at result files
ls -l *windowed.weir.fst


#send these to pungitius_exercise/ on personal computer to plot with R