Question

How can I compare the structural variation detecting ability between each different tools?

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9.5 years ago

lee.jingu0626 ▴ 50

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.

sequencing Assembly next-gen alignment • 2.4k views

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 9.5 years ago by lee.jingu0626 ▴ 50

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Check in an alignment viewer.

ADD REPLY • link updated 2.3 years ago by Ram 43k • written 9.5 years ago by lh3 33k

Ram · Answer 1 · 2014-10-16

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9.5 years ago

mangfu100 ▴ 800

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 COMMENT • link updated 2.3 years ago by Ram 43k • written 9.5 years ago by mangfu100 ▴ 800

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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 REPLY • link 4.9 years ago by vaish01kv • 0