PennCNV-Affy cluster generation for chrX/chrY in gender-specific cancer types

Question

[Charles Warden]

Hi,

I have encountered a problem using PennCNV-Affy to call BAF/LRR values in cancer types that are exclusively one gender (for example, ovarian cancer). More specifically, it looks like the problem occurs at the cluster generation step, where I see the following error (and clusters are not defined for chrX or chrY):

WARNING: unable to find enough males (count=0) and females (count=n) for chrX/chrY cluster generation (use --sexfile to supply this information)

I have tried setting --min_subject equal to 0, and I still get the same error message. I checked and the sex chromosome probes have been properly processed for all of the input files.

Here is the command that I am using:

/path/to/generate_affy_geno_cluster.pl \
  /path/to/birdseed.calls.txt \
  /path/to/birdseed.confidences.txt \
  /path/to/quant-norm.pm-only.med-polish.expr.summary.txt \
  -locfile /path/to/affygw6.hg38.filter.pfb \
  -sexfile /path/to/CRLMM_gender_file.txt \
  --min_subject 0 \
  -out /path/to/gw6.genocluster.hg38

Any recommendations? If nothing else works, I assume that I can use the pre-defined cluster file (hapmap.genocluster), but I'd prefer to define the clusters using my own samples.