Question: How can I compare the structural variation detecting ability between each different tools?
0
gravatar for lee.jingu0626
4.9 years ago by
Korea, Republic Of
lee.jingu062630 wrote:

Hi everyone.

I have one question about comparison between each different tools.(DELLY, CREST)

I performed these two tools in same tumor data. 

So, I want to know the reason that some variation detected by DELLY but, in the same time, CREST can't detect that variation. Also in the opposite situation I wonder about that.

How can I confirm these situation? Just compare between DELLY's source code and CREST's source code?

Are there any efficient method? I'm confusing because of this problem. So please let me know how I can find the reason.

Thank u for reading my question.

ADD COMMENTlink modified 4.9 years ago by mangfu100710 • written 4.9 years ago by lee.jingu062630

Check in an alignment viewer.

ADD REPLYlink written 4.9 years ago by lh331k
1
gravatar for mangfu100
4.9 years ago by
mangfu100710
Korea, Republic Of
mangfu100710 wrote:

Why don't you choose another reliable variants calling "FACTERA: a practical method for the discovery of genomic
rearrangements at breakpoint resolution".

I recommend using above tool due to its high sensitivity.

Using three different types of tools would be more beneficial to you in your research.

 

ADD COMMENTlink written 4.9 years ago by mangfu100710

How to interpret the output of "FACTERA"? I'm finding it difficult to figure out false positives. Also where can i find the ranking ? Which rearrangement has most impact on the disease?

ADD REPLYlink modified 3 months ago • written 3 months ago by vaish01kv0
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