search

etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
Other
502 stars 162 forks source link

bin size for targeted amplicon sequencing #480

Open yuyuliu opened 4 years ago

yuyuliu commented 4 years ago

I am applying CNVkit to targeted amplicon sequencing data by following your command:

cnvkit.py batch -m amplicon -t targets.bed *.bam

Is this command using the default bin size of 200? Some of my amplicons are only 100 or 150bp, should I change the bin size or not?

etal commented 4 years ago

That command should be fine. The default bin size is just a suggestion to CNVkit; it will subdivide larger contiguous regions into bins of approximately 200bp, but it won't alter bins/targets smaller than that.