Why are structural variants typically not tagged as well as SNPs?
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6 months ago
curious ▴ 520

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?

wgs imputation structural variation • 179 views
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In my experience: too many false positives, it's hard to compare two SV.

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So its a SV calling issue that leads to noise and this is why SV are less correlated with SNPs?

I was actually wondering if there was some type biological explanation for why SVs are not a easy to tie to a specific haplotype, but I really couldn't think of one. You explanation would make sense, assuming I understand it correctly. It would kind of make sense with what I understand about SV calling, is that it is hard and needs lots of different callers to produce one reliable consensus call.

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I guess the other thing is that if these SVs are in very unstable regions maybe they just keep getting messed up with each generation at a rate that makes them difficult to be reliably correlated with any SNV?

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