From: Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
Software
Number CNVs
Duplications
Deletions
Median Number CNVs per patient (Min, 25%, 75%, Max)
CRLMM/VanillaIce
45,757
7,958
37,799
30 (4, 21, 42, 438)
PennCNV
50,908
16,132
34,776
39 (13, 31, 48, 96)