Question: How can I confirm structural variation is correct?
0
gravatar for lee.jingu0626
4.4 years ago by
Korea, Republic Of
lee.jingu062630 wrote:

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!

next-gen • 1.5k views
ADD COMMENTlink modified 4.4 years ago by Robert Sicko540 • written 4.4 years ago by lee.jingu062630

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

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

ADD REPLYlink written 4.4 years ago by Devon Ryan87k

No. he is my lab fellow.

I am still waiting somebody to reply my question.

ADD REPLYlink written 4.4 years ago by mangfu100640

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

ADD REPLYlink written 4.4 years ago by Devon Ryan87k
2
gravatar for William
4.4 years ago by
William4.3k
Europe
William4.3k wrote:

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.

 

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by William4.3k
1
gravatar for Robert Sicko
4.4 years ago by
Robert Sicko540
United States
Robert Sicko540 wrote:

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

ADD COMMENTlink written 4.4 years ago by Robert Sicko540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1242 users visited in the last hour