PennCNV-Affy substep 1.3 cluster generation for chrX when all samples are female?

[Lydia-King]

Hello,

I am using PennCNV-Affy to generate the LRR and BAF values from Affymetrix SNP 6.0 CEL files. I'm using PennCNV-Affy on ~1,900 CEL files generated from breast cancer samples and so all my samples are labelled as female in the sexfile. When I run substep 1.3 of the PennCNV- Affy pipeline to generate the canonical genotype clustering file I get the following message:

WARNING: unable to find enough males (count=0) and females (count=1992) for chrX/chrY cluster generation (use --sexfile to supply this information)

I have tried setting the min_subject argument to 0, and I still get the same error message. Furthermore as a sanity check, I changed some of the samples to males in the sexfile and it worked as expected for that, so the issue seems to be when there is only 1 sex present.

Here is the command that I am using:
$Program_Geno_Cluster $Birdseed_Calls $Birdseed_Conf $Quant_Norm -locfile $AffyHg -sexfile $filesex -min_subject 0 -out ../apt_$1_$2/gw6.genocluster

Any ideas/suggestions would be greatly appreciated.
Thank you!