Hello,

I am performing GWAS in a subset of population which consists of about 250 individual cases. I am running GWAS and association studies on SNP data.

All the results I get are underinflated despite strong population stratification and removal of cryptic relatedness.

• Population Stratification - I am sub setting the population based on their racial makeup
• Cryptic relatedness - I am accounting for this using the --indep-pairwise command in plink.

The QQ-Plot in Locus Zoom yields a like that is deflated. No matter the --maf value, or the population stratification, I cannot yield an output that aligns with the QQ-plot line.

I wonder if Plink under performs with low data points.

I am new to this. Please excuse any basic errors I've made in this post.

Thank you, Soren Basnet.