For GWAS analysis, we get different significant points on SNP-based, and Indel-based GWAS. In my opinion, it is understandable, because we conducted exome sequencing. The associated SNP or Indel are dependent event, thus the different pattern are normal. But I got the comments, the variant are just as genetic markers. Either SNP or Indel based GWAS, the significant peaks will not be different.

Actually, I can not understand why? The marker density, marker type and marker locations are totally different.

😆

If it is QTL analysis, I can understand why.