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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Add 'GC fraction for bad bins masking' to PARAMS #753

Closed tetedange13 closed 1 year ago

tetedange13 commented 1 year ago

Should adress #738.

Maybe my comment above new MASKED_GC in params.py could be more explicit about the fact that you set a single value, which is used to perform a symetric filtering ? [eg.: "0.3" filters bin with GC-content "less than 0.3" and "above (1-0.3)=0.7"]

etal commented 1 year ago

I like this solution. Would you be able to update this PR to specify two thresholds (GC_MIN_FRACTION, GC_MAX_FRACTION) instead of assuming symmetry?

tetedange13 commented 1 year ago

Done @etal ! :)

Have a nice day ! Felix.

etal commented 1 year ago

Awesome, thanks so much!