Genome Wide Association analysis (GWAS)

To test the association of of a genome-wide set of genetic variants with a given trait.

install vcftools

  git clone
  cd vcftools
  sudo make install

Install R and RStudio

  sudo apt-get update && sudo apt-get install -y gdebi-core r-base r-base-dev
  sudo gdebi -n rstudio-server-1.0.143-amd64.deb

Make a working directory for the GWAS analysis

  mkdir ~/GWAS && cd ~/GWAS

Download the sample VCF file and phenotype data

Genotyping of 476840 SNPs in 53 dogs (24 yellow coat and 29 dark coat)

  gunzip pruned_coatColor_maf_geno.vcf.gz

create list of alternative alleles

  cat pruned_coatColor_maf_geno.vcf | awk 'BEGIN{FS="\t";OFS="\t";}/#/{next;}{{if($3==".")$3=$1":"$2;}print $3,$5;}'  > alt_alleles

Run a simple association analysis

–assoc performs a standard case/control association analysis which is a chi-square test of allele frequency.
By default, the minor allele is coded A1 and tested for being the risk allele. The minor allele is expected to be the alternative allele but could happen to be the reference one. –reference-allele allow you to use your list of A1 alleles
–adjust enables correction for multiple analysis and automatically calculates the genomic inflation factor
  plink --bfile coatColor.binary --make-pheno coatColor.pheno "yellow" --assoc --reference-allele alt_alleles --allow-no-sex --adjust --dog --noweb --out coatColor

Create Manhattan plot

Install qqman package

sudo Rscript -e "install.packages('qqman',  contriburl=contrib.url(''))"

Identify statistical cutoffs

unad_cutoff_sug=$(tail -n+2 coatColor.assoc.adjusted | awk '$10>=0.05' | head -n1 | awk '{print $3}')
unad_cutoff_conf=$(tail -n+2 coatColor.assoc.adjusted | awk '$10>=0.01' | head -n1 | awk '{print $3}')

Run the plotting function

Rscript -e 'args=(commandArgs(TRUE));library(qqman);'\
'data=read.table("coatColor.assoc", header=TRUE); data=data[!$P),];'\
'bitmap("coatColor_man.bmp", width=20, height=10);'\
'manhattan(data, p = "P", col = c("blue4", "orange3"),'\
'suggestiveline = 12,'\
'genomewideline = 15,'\
'chrlabs = c(1:38, "X"), annotateTop=TRUE, cex = 1.2);'\
';' $unad_cutoff_sug $unad_cutoff_conf

The top associated mutation is a nonsense SNP in MC1R (c.916C>T) known to control pigment production. The file coatColor_man.bmp can be visualized with RStudio or downloaded to your local computer (from local commandline) via: scp username@ipaddress:/home/username/GWAS/coatColor_man.bmp .