Very minor issue, but it looks like you're plotting ALL of your associations in your manhattan plots, rather than just the genotype associations. To clarify: when you run your GWAS, you include the top PCs as covariates in the regression (this is correct). But this means that you also get regression results for the covariates, not just the variants you're testing. Take a look at the TEST column in the .assoc.linear output file(s) of the plink --linear command to figure out which results you want to keep/plot.
README.md
with commands and analyses2/2
plotting.py
script to produce plots3.75/4
Very minor issue, but it looks like you're plotting ALL of your associations in your manhattan plots, rather than just the genotype associations. To clarify: when you run your GWAS, you include the top PCs as covariates in the regression (this is correct). But this means that you also get regression results for the covariates, not just the variants you're testing. Take a look at the
TEST
column in the.assoc.linear
output file(s) of theplink --linear
command to figure out which results you want to keep/plot.Pretty plots
4/4
Grade
Total: 9.75/10
Nice work!