Hello everybody,
Several tools have been developed for the detection of structutal variants in genome data since 2009. I would like to focuse on the case of somatic structural variants.
The most commonly used tools are probably BreakDancer, Pindel, Delly, Novobreak, SquareDancer and SVDetect. And maybe some others.
I recently got 20 paired normal tumor genome data. I am looking for the "best tools" to use in my case.
My case: 101bp paired-ends reads. Coverage ~30x for each sample. I am working on leukemia. Almost 100% of tumor in the tumor sample but I can have tumor contamination in the normal sample (from 0 to 20%).
I intend to use BreakDancer and Pindel. They seem complementary for the size of indels they are able to detect.
Regarding my data, do you any advice/recommendations?
Do you think I should prefer other tools?
Thank you in advance,
Jane
Several tools have been developed for the detection of structutal variants in genome data since 2009. I would like to focuse on the case of somatic structural variants.
The most commonly used tools are probably BreakDancer, Pindel, Delly, Novobreak, SquareDancer and SVDetect. And maybe some others.
I recently got 20 paired normal tumor genome data. I am looking for the "best tools" to use in my case.
My case: 101bp paired-ends reads. Coverage ~30x for each sample. I am working on leukemia. Almost 100% of tumor in the tumor sample but I can have tumor contamination in the normal sample (from 0 to 20%).
I intend to use BreakDancer and Pindel. They seem complementary for the size of indels they are able to detect.
Regarding my data, do you any advice/recommendations?
Do you think I should prefer other tools?
Thank you in advance,
Jane
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