A great set of tools for manipulating and analyzing VCF files
This exercise should be run on your personal computer
Instructions for installing VCFtools are here:
Download this file to your desktop, unzip it, then follow instructions below
Or copy over on TACC:
#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 less chr1_Fst_results.weir.fst less chr12_Fst_results.weir.fst #Use plot_Fst.R to plot the results ./plot_Fst.R #look at the resulting plots ls *Fst_plot.pdf open *.pdf #What is biological explanation for these results?