Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-23T16:57:24.333Z
Answers.LastActivityDate: 2021-08-23T16:57:24.333Z
Answers.UserDisplayName: Florian
Body: <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>
  
Tags: <wgs><illumina><cnv><somatic>
Title: polidy VCF file for Canvas somatic-wgs cnv calling
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  