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A great set of tools for manipulating and analyzing VCF files

This exercise should be run on your personal computer

Installing vcftools:

Instructions for installing VCFtools are here:


Download this file to your desktop, unzip it, then follow instructions below

Exercise Files

Or copy over on TACC:



vcftools --weir-fst-pop
#Navigate to the exercise directory 
cd ~/Desktop/vcftools
#Look at the input files:
ls *.vcf
ls *.txt
#look at the genotype data for chromosome 1
less chrI.vcf    
#look at the genotype data for chromosome 12
less chrXII.vcf    
#a list of the male samples in the VCF 
less male_pun.txt
#a list of the female samples in the VCF
less female_pun.txt
#Use VCF tools to get Fst between males and females for the two VCF files
vcftools --vcf chrI.vcf --weir-fst-pop male_pun.txt --weir-fst-pop female_pun.txt --out chr1_Fst_results
vcftools --vcf chrXII.vcf --weir-fst-pop male_pun.txt --weir-fst-pop female_pun.txt --out chr12_Fst_results

#look at the results
ls -l *.fst

#Use plot_Fst.R to plot the results

#look at the resulting plots
ls *Fst_plot.pdf
open *.pdf

#What is biological explanation for these results?