Using RADseq to determine copy number and allele frequencies at duplicated loci

Perhaps there is hope yet for using RAD to estimate genomic copy number and allele frequency of duplicated loci; see this approach from cancer genomics.  It compares RADseq to exome and whole-genome sequencing for estimates copy number and allele frequency of duplicated regions.

That said, they have access to resources we don’t (i.e. a full reference sequence), and collapse adjacent sites, but at least it is a start.


Caihong Zheng et al.

Determination of genomic copy number alteration emphasizing a restriction-site based strategy of genome re-sequencing

Bioinformatics first published online August 20, 2013 doi:10.1093/bioinformatics/btt481