CNVKit for unmatched tumor-only WGS samples
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16 months ago
vctrm67 ▴ 30

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

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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.

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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.

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vctrm67

Were you able to find a solution for this ?