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Possible bug in bin sizes #904

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gevro opened this issue Aug 11, 2024 · 0 comments
Open

Possible bug in bin sizes #904

gevro opened this issue Aug 11, 2024 · 0 comments

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@gevro
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gevro commented Aug 11, 2024

Hi,
I ran the latest version of cnvkit via docker with these settings:

cnvkit.py batch -n -f REF.fasta -m hybrid -g ACCESSIBLEREGIONS.bed -t PROBESBED.bed --target-avg-size 50000 --antitarget-avg-size 4000000 --antitarget-min-size 1000000

However, it is producing a target.bed file whose average bin size is only 122.79 bp. This should not be possible based on the above settings.

This is with hg38.

So there appears to be a bug in the way batch interprets these parameters:
--target-avg-size 50000

Or is this because bins cannot encompass more than one target? If so, I assume then that the segment step integrates information across multiple bins?

Thanks

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