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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.

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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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