vcftools

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:

https://vcftools.github.io/downloads.html

Exercise:

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

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
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?