Dot programming to draw cryptic relationships from GWAS samples

One of the confounding factors in GWAS is genetic relatedness between the samples. PLINK offers utilities to find relatedness and filter samples as per degree of relatedness you wish to exclude for statistical association analysis. As often GWA studies involve larger number of unrelated samples, it becomes very hard to manually draw relationship between the samples, especially when the population in question is highly inbred. In this context one can make use application of DOT programming to draw directed graphs and select unrelated individuals from the cluster of related individuals, quite easily. To do so
Get second and fourth column from your PLINK IBD command output filename.genome.

awk –F “ ” ‘{print $2,$4}’ FileName.genome > CrypticRel.dot

Then insert ‘->’ between the sample ids

sed –i ‘%s/\s/->/g’ CrypticRel.dot

Then, add following lines to top of the file CrypticRel.dot

Diagraph CrypticRelatedness {
Graph [splines=true overlap=false center=1];
Node [shape=none];

By,

sed –i ‘1i \
           Diagraph CrypticRelatedness {\n
      Graph [splines=true overlap=false center=1];\n
           Node [shape=none]; \n
      ’ CrypticRel.dot

Then, add '}' at the end of the script

sed –i ‘$a\}’ CrypticRel.dot

Then, execute crypticRel.dot as follows

circo CrypticRel.dot –Tpng:gd –o CrypticRel.png

Now carefully look at the samples network and decide who to retain for further analysis.