Does PennCNV handle non-polymorphic probes?
Yes. In principle, it can also handle oligonucleotide arrays without SNP markers. There are two ways to represent non-polymorphic probes: (1) if the marker name contains the word “cnv” (for Illumina arrays) or “CN” (for Affymetrix arrays), they will be treated as non-polymorphic markers by PennCNV. (2) if the allele frequency annotation in the PFB file for a marker is more than 1, then this marker will be treated as a non-polymorphic marker by PennCNV program. The second situation is suitable for custom designed arrays.
