<p>It seems you need to supply vcf files specifying the ploidy of the sex chromosomes.</p>
<p>See <a href="https://github.com/Illumina/canvas/issues/89" rel="nofollow noreferrer">https://github.com/Illumina/canvas/issues/89</a> for explanation and example vcf files.</p>

CC BY-SA 4.0
2021-08-23T16:57:24.333Z
2021-08-23T16:57:24.333Z
Florian
<p>I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option &quot;--ploidy-vcf&quot; which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV.vcf file from the germline WGS (matched normal run on Canvas smallPedigree), but it has given an error that says &quot;Reference copy number &gt; 2 is not supported&quot; at the last stage of run.</p>
<p>I would like to know your experience when you used CANVAS on somatic WGS samples. What ploidy-file is appropriate here? Should it be only chrX and Y in it? Your suggestions please.</p>

<wgs><illumina><cnv><somatic>
polidy VCF file for Canvas somatic-wgs cnv calling
# polidy VCF file for Canvas somatic-wgs cnv calling

(Asked by: username_0 on 2021-05-20)

I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option "--ploidy-vcf" which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV.vcf file from the germline WGS (matched normal run on Canvas smallPedigree), but it has given an error that says "Reference copy number > 2 is not supported" at the last stage of run.

I would like to know your experience when you used CANVAS on somatic WGS samples. What ploidy-file is appropriate here? Should it be only chrX and Y in it? Your suggestions please.

**Tags:** wgs, illumina, cnv, somatic

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## 1 answers

### Answer by username_1 on 2021-08-23. Score: 1

It seems you need to supply vcf files specifying the ploidy of the sex chromosomes.

See <https://github.com/Illumina/canvas/issues/89> for explanation and example vcf files.


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