call with filters cn, ci, sem

etal / cnvkit

Copy number variant detection from targeted DNA sequencing

http://cnvkit.readthedocs.org

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call with filters cn, ci, sem #906

Open gevro opened 2 months ago

gevro commented 2 months ago

Hi, I'm trying to run call with --filter cn --filter ci --filter sem. But getting this error: ValueError: 'sem' filter requires column 'sem'

However, I ran segmetrics with --ci and --sem.

etal commented 1 month ago

Hmm. In the .cns emitted by segmetrics, is there another column generated with a name similar to "sem"? If the column names diverged, that would be a simple bug to fix.

gevro commented 1 month ago

The .cns file output by segmetrics has a column 'sem'. So I'm not sure why the call program is not working with sem. Suggests the bug might be in the 'call' program.