Question: can I use CNVkit for calculating copy number differences in different human population sample data for selected regions?
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gravatar for jainythomas1
3.9 years ago by
jainythomas110
jainythomas110 wrote:

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

cnv cnvkit • 1.0k views
ADD COMMENTlink modified 3.9 years ago by Eric T.2.6k • written 3.9 years ago by jainythomas110
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gravatar for Eric T.
3.9 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Eric T.2.6k
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