can I use CNVkit for calculating copy number differences in different human population sample data for selected regions?

Question

[jainythomas1]

Hi Etal,

Can I use CNVkit to calculate the copy number difference in some particular regions of the human reference genome and in comparison with other human genome samples generated population studies?

Please let me know if you need more details Thank you

Answer 1

[Eric T.]

The common CNVs seen in populations studies tend to be smaller than what CNVkit detects reliably in typical sequencing data. But if you're able to get good CNV calls from WGS using CNVkit, great. The UCSC Genome Browser has a human CNV track, so you can export your CNVkit calls to BED format (cnvkit.py export bed) and upload to compare and identify overlaps with that track.