jeltje/dnacopy repository overview

Input is adtex cnv.results, SD, and sample ID. Outputs to stdout

The default Adtex copynumber settings do not work, likely because the scores are not in log space. This post processing step creates longer segments from the exon scores, ignoring the segment scores in the Adtex output.

Details: https://www.bioconductor.org/packages/3.3/bioc/vignettes/DNAcopy/inst/doc/DNAcopy.pdf⁠ Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK. Inferring copy number and genotype in tumour exome data. BMC Genomics. 2014 Aug 28;15:732 http://www.ncbi.nlm.nih.gov/pubmed/25167919⁠