SegCNV is a software package, implemented in C++, to detect germline copy number variations in SNP array data. Currently, SegCNV supports Illumina 550K and 610K genotyping platforms
HadoopCNV (internal codename: PennCNV3) is a Java implementation of MapReduce-based copy number variation caller for next-generation whole-genome sequencing data.
PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.
PennCNV-2 is the second major release of the popular program PennCNV, which was originally designed for inferring copy number variation in germline DNA using data from genotyping microarrays. PennCNV-2 now supports inference of copy number abberrations in tumor cells (PennCNV-tumor).
PennCNV-Seq is an adaptation of the original PennCNV algorithm for whole-genome sequencing data.
de Araújo Lima L, Wang K. PennCNV in whole-genome sequencing data.
BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):383. doi: 10.1186/s12859-017-1802-x. PMID: 28984186; PMCID: PMC5629549.