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How And Where To Retrieve The Cnv Information From The Breakdancer Results

Hi everybody As known, breakdancer uses the pair end way to call cnv. Its readme file says that with the CPP version, it's possible to call the copy number variants. However, I only found INS, INV, DEL, ITX, CTX five aberration types in the results. Anybody could tell me where I could find the cnv results information. Thanks in advance.

breakdancer cnv
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updated by Chris Miller Chris Miller • written by luofei.whu • luofei.whu

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Breakdancer doesn't call copy number variants. It calls structural variants. If you see a large deletion in breakdancer, it may be the case that a copy number deletion has occurred. It's also possible that the deleted sequence got re-integrated somewhere else, in which case, there would be no effect on copy number.

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written by Chris Miller Chris Miller

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