text: user12038: 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.
  
  user14026: 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.
  
original_text: 12038: <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>
   14026: <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>
  