Question: How to identify structural variants manually?
2
gravatar for mangfu100
5.2 years ago by
mangfu100720
Korea, Republic Of
mangfu100720 wrote:

Hi. 

I have a question from using pipeline that find the structural rearrangements like SVDetect or BreakDancer.

I ran above software and now I am having a results from SVDetect and BreakDancer.

(Input files is a tumor bam file based on paired end and output files is just a txt file.)

Results have many columns that describe the sequence information like start position, end position, class of

type(indel, translocation,duplication  and etc...).

I almost understand why these types are classified by software. 

However, I want to see manually that really my tumor bam file has the structural variation which is previously

classified by software.

For example, I used SVDetect which find structural variants and got a output result and its content is below.

chr10 255485 255896 chr10 255738 256047   (F,F,F,F,F,F) (R,R,R,R,R,R) TRANSLOC

As i mentioned, I already understood the information above conceptually. but my ultimate goal is just want to identify whether TRANSLOC really happened at above position in tumor bam files or not.

Because many software has mis classification. Therefore, It is required for me to see variants manually not only seeing the output file.

Anyway my question is how you validate the output files ?

If you have your own validate process.. could you explain me in detail?

I heard the IGV program and I already used this tool but i can't find anything information that i want. 

I am looking forward to you reply.

Thank you

 

 

 

 

alignment next-gen gene • 1.6k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 5.2 years ago by mangfu100720
5
gravatar for Sean Davis
5.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

IGV is definitely a good tool for this task.  There are some details that might be applicable here:

http://www.broadinstitute.org/igv/interpreting_pair_orientations

Just FYI, running the structural variant detection on the "normal" sample from the same patient or a pool of "normals" can very greatly reduce your false positive results if you exclude any SV in the tumor that is overlapping one in the normal (or normals).

ADD COMMENTlink written 5.2 years ago by Sean Davis25k
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