Hello, everyone!

I am working with inbred (6-7 generations) plant lines and try to make the GWAS analysis. But I face the following issue: there are sites in my VCF that are heterozygous for all samples and it is quite strange. I also saw a thread on a Biostars ( https://www.biostars.org/p/75819/#75826) and as I understood it is a quite common situation for GATK. So is it ok to simply remove such suspicious sites from the analysis? And if so have you seen such some publications where it is done so?