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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Don't give warning when no/little reads map to antitarget region. #487

Open dodoflyy opened 4 years ago

dodoflyy commented 4 years ago

Here 

Processing antitarget: AHKYT7DSXX_S73_L001_BQSR
Keeping 0 of 40893 bins
WARNING: most bins have no or very low coverage; check that the right BED file was used

I don't think this should give warning. It's normal thing that little reads cover antitarget region.

etal commented 4 years ago

If you used hybrid capture, then there should be at least a few reads in the antitarget regions. The warning usually kicks in when off-target coverage is vanishingly low. Do you know your off-target coverage in this sample?

This check is in place to see if you used ran the pipeline for hybrid capture (default, batch -m hybrid), but the sequencing data actually came from targeted amplicon sequencing where there are truly no off-target reads. In the latter case, you can use batch -m amplicon to skip antitargets.