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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Update hmm.py, make the window paramter activate of segment_hmm function #835

Closed zhuying412 closed 10 months ago

zhuying412 commented 11 months ago

make the window paramter activate of segment_hmm function

833

etal commented 11 months ago

Thanks, @Zhu-Ying . Was this change enough to fix the false negative you saw in #833 ? Did it improve your results overall, and not cause any other false positives or negatives elsewhere?

zhuying412 commented 10 months ago

Thanks, @Zhu-Ying . Was this change enough to fix the false negative you saw in #833 ? Did it improve your results overall, and not cause any other false positives or negatives elsewhere?

Yes, if I set the window=2, I can get more CNVs which is smaller size，and the false negative CNV can be called. the window is larger, the sensitivity is lower. I don't know why, but it works. I think it will produce some false positives, but we need lower false negatives in clincal. we just want to make the -t (threshold/window) parameter actived，now the code is commented.

etal commented 10 months ago

Great, thanks for your contribution!