Figure 4

Comparison of genotyping results generated by BCRgt, BRLMM and BCRgt with correct and incorrect copy number data. Correct copy number data were used for (a)-(d), and incorrect copy number data (we intentionally call copy number loss regions as normal regions) were used for (e) and (f). (a) SNPs with “AB” genotype called by BCRgt on a sample with multiple copy number losses on chromosomes 1, 4, 6, 8, 10, 12–14, 16–18, 21 and 22. (b) SNPs called “AA”/“BB” by BCRgt. (c) SNPs called “AB” by BRLMM. (d) SNPs called “AA”/“BB” by BRLMM. (e) SNPs with “AB” genotype called by BCRgt, but we intentionally misclassified the CNA status. (f) SNPs with “AA/BB” genotype called by BCRgt.