About SNP-based and Indel-based GWAS

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4.2 years ago

r00628112 ▴ 10

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.

Manhattanplot • 1.1k views

ADD COMMENT • link updated 4.2 years ago by Kevin Blighe 88k • written 4.2 years ago by r00628112 ▴ 10

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Why not treat them as the same variable type for the purpose of the GWAS / eQTL? I see no reason to perform an analysis stratified by SNP and indel.

ADD REPLY • link 4.2 years ago by Kevin Blighe 88k

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