CNVKit for unmatched tumor-only WGS samples

Question

[vctrm67]

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.

[igor]

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

[vctrm67]

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

[igor]

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.

[vctrm67]

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.

[lakhujanivijay]

vctrm67

Were you able to find a solution for this ?

[rohitsatyam102]

Yeah, I am also stuck with it. Did anyone here find a way?