I'm tring to identify recurrent DNA copy number change using dChip, DNAcopy and GISTIC from a set of SNP 6.0 data, which was suggested in paper "Subgroup-specific structural variation across 1,000 medulloblastoma genomes". As we known, SNP 6.0 has two sets of marker, i.e. SNP marker and copy number (CN) marker. dChip treats these two marker sets separately, and output their raw copy number in two files, one is for SNP marker, the other is for CN marker. However, the DNAcopy software (use to segment the copy number profile) seems to can only use the dChip SNP marker output file as input, because its input file only have one colume of marker position (just the same as dChip SNP marker output file), while the dChip CN marker output file has two position columes (Start and End). I'm not sure whether DNAcopy can make use of the CN marker information of SNP6.0. Is there anyone know about that?
Best, Jian-You Liao