Question: CNVKit for unmatched tumor-only WGS samples
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gravatar for vctrm67
7 weeks ago by
vctrm6720
vctrm6720 wrote:

Does anyone know how to use cnvkit on tumor-only WGS samples? I tried making a flat reference using b37 but I cannot without a target/antitarget bed file, which I don't have for an entire genome.

cnvkit • 144 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by vctrm6720

Did you check the docs? https://cnvkit.readthedocs.io/en/stable/nonhybrid.html

ADD REPLYlink written 7 weeks ago by igor12k

Yes. There is no mention of what to do for this specific case.

ADD REPLYlink written 7 weeks ago by vctrm6720

Isn't this what you are looking for?

The batch --method wgs option uses the given reference genome’s sequencing-accessible regions (“access” BED) as the “targets” – these will be calculated on the fly if not provided. No “antitarget” regions are used.

ADD REPLYlink written 7 weeks ago by igor12k

I looked at that, but you can see that they use the -n tag, whereas I do not have any normals. I need to use the -r tag:

  -r REFERENCE, --reference REFERENCE
                        Copy number reference file (.cnn).

However, I cannot seem to generate a .cnn file without a target/antitarget file, which I don't have since this is WGS and I can't find one for b37.

ADD REPLYlink written 7 weeks ago by vctrm6720
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