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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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What is the default target-avg-size for wgs? #691

Closed ytakemon closed 2 years ago

ytakemon commented 2 years ago

Hello! Firstly, thanks for building this tool and I am finding your documentation very helpful!

I was wondering when using default settings batch -m wgs what is the “target” average bin size (--target-avg-size)?

I noticed in the doc you explained that the --target-avg-size can be increased and that batch -m wgs option does this, but it wasn't clear to me what the default size would be when nothing is specified.

etal commented 2 years ago

It can vary. If you run batch with one or more normal samples, it will estimate a reasonable bin size based on the average read depth of the normal samples; the math is in the autobin command and it will print out the calculated bin size during processing.

Without normal samples, in wgs mode, the default is 5000bp: https://github.com/etal/cnvkit/blob/master/cnvlib/batch.py#L78

ytakemon commented 2 years ago

Thank you!