PennCNV - CNV detection from Illumina whole-genome SNP genotyping arrays and more

PennCNV is a software originally developed for CNV detection from Illumina whole-genome SNP genotyping arrays. It has been extended to handle candidate gene SNP arrays, to handle recent high-density arrays with non-polymorphic markers (so-called CN markers), and to handle Affymetrix genome-wide arrays.

PennCNV is available using the command:

module load penncnv

Executables are convert_cnv.pl, genomic_wave.pl, etc.