The assumption that copy number is an integer allows for predefined, strongly modeled states to increase sensitivity. For both SNP probe sets and copy number probes, these emission probabilities allow us to estimate the relative likelihood of each possible copy number level (0, 1, 2, 3 or 4) in a way that is informed by the specific performance of each probe. We note that although this considerably improves performance when assessing germline copy number, it may make Birdseye less suitable for applications where average copy number at a locus is noninteger (such as detection of mosaic copy number changes in heterogeneous tumor DNA).
