What happens when SNV caller looks at a SV (e.g. deletion) region?

Question

[DVA]

Hello,

I hope this question is not too silly. What would happen to SNVs callers such as GATK, if a region has some kind of structure variations? Would the caller be able to tell?

Thank you!

[lakhujanivijay]

No question is silly until it is framed properly. It's silly when you don't dare to ask.

Anyways, have a look at the below related posts

Structural Variation Detection Using Gatk

GATK page

Answer 1

[WouterDeCoster]

I'll assume you are talking about short read sequencing. SNV callers should be capable to detect small indels, such as an insertion of a couple of nucleotides. For an SNV caller there is only something noticeable at the breakpoints in the case of an SV - so it is possible that an SNV or small indel is called there rather than the larger event (and as such it is misrecognized). But "inside" the larger deletion (for example) the SNV caller won't notice anything. At best you can identify a stretch with Loss-Of-Heterozygosity (if it's a large deletion). Things also depend on the aligner, and how that tool handles SVs. Another complication is that most SVs will be in repetitive regions - which are inherently messy for short read alignment and therefore also SV calling from short reads. Furthermore, SV callers will for example also look at split reads, soft-clipped read ends and depth of coverage to identify the presence of an SV, while as far as I know, SNV callers don't.

[DVA]

Thanks so much! I appreciate your help.