GWAS analysis with truncated gene phenotype

Question

[3335098459]

Hi,

I have performed a pangenome analysis on NCBI downloaded genome and found various strains with a specific truncated gene(s) that will surely result in a change in phenotype.

Lets say if we consider the phenotype a beginning point and perform a GWAS analysis (to find out other affected genes) by using SCOARY and pyseer.

Would this be a good idea to undermine or know more about the effects of the truncated gene?

Regards

Awan