Figure 4.

Coverage, purity, and alterations affect the B-allele frequency of SNPs. B-allele frequencies (BAF) of germline heterozygous SNPs can be used to identify copy number aberrations. A–F show that the BAF is noisy, and that it gets increasingly more difficult to separate the bands as the purity or coverage goes down and when the aberration is subclonal. To reduce the noise, SNPs can be phased to determine which allele is the B-allele. By combining the SNPs over longer stretches of DNA it becomes possible to detect subclonal aberrations.