I've wondered this for a really long time and I don't know where else to ask. Why are structural variants generally not tagged as well as SNPs?
Take this excerpt from and Ira Hall paper:
"Notably only 58.2% of common, autosomal SVs ... were in strong LD (r2 ≥ 0.8) with a SNV or indel ascertained by WGS in our study, compared to 79.4% of common SNVs"
I don't understand how this could be mechanistically. Does anyone know?