How can I confirm structural variation is correct?

Question

[lee.jingu0626]

Hi.

I have one question.

I found the structural variation with SVDetect and NGS data. So I can check a lot of variation.

But I don't know how can I confirm those structural variation is exactly correct.

I found the Indel in some chromosome region, but I think it is possible to just error through sequencing alignment.

So I want to know how can I check that. Please give me some methods!

[Devon Ryan]

This looks suspiciously like this question: How to identify structural variants manually?

Am I correct in guessing that you're the same user?

[mangfu100]

No. he is my lab fellow.

I am still waiting somebody to reply my question.

[Devon Ryan]

OK, just checking. William's reply (below) is relevant to your question as well.

Answer 1

[William]

You can visually inspect the SV call regions in Savant which gives nice plots like these:

Loading a bed file with the low complexity and repeat regions of your genome of interest also helps with the visual inspection.

http://genomesavant.com/p/home/index

Reliable SV calling is still pretty much a research subject and you can expect a lot of false positive and false negative calls. Most people prefer to have false negatives so they are very strict about accepting SV calls and require evidence from multiple signals (depth, discordant pair, split-read / contig) and multiple tools to accept SV calls.

Some recent SV callers already use multiple signals for more reliable SV calling. Delly is an example that uses discordant pair and split-read https://github.com/tobiasrausch/delly

In the end you can design primers and sequence over the breakpoint(s) to be more sure about the SV's.

Answer 2

[Robert Sicko]

If you are talking about validating a larger region (>1000bp?) you could use Taqman Copy Number assays to validate the predicted copy-number (or manually designed qPCR to predict copy-number).

Also see: Confirming Structural Variants In The Genome