Fig. 5

Comparison of BaalChIP with other available methods. Left y-axis corresponds to the frequency of ASB events called by BaalChIP or the binomial tests (red, blue and purple lines). Right y-axis corresponds to the mean of the posterior probability given by the iASeq method (black line). The numbers at the top of the plot show the total number of tested heterozygous sites in each bin. a SNPs were grouped in bins of different RAF intervals. The RAF intervals increase in terms of distance to the diploid value (RAF = 0.5). The binomial test (without RAF correction; purple line) and the iASeq methods (black line) are biased towards the detection of ASB events in regions of altered copy numbers. b SNPs were grouped in bins of different depth of coverage. SNPs in regions RAF < 0.4 or RAF > 0.6 were excluded from this analysis. When applying the binomial test (purple and blue lines), the frequency of ASB detection increases for higher covered sites, while the same is not true when applying BaalChIP or the iASeq methods. The effect is particularly visible for the FAIRE-seq data set. ASB allelic-specific binding, binom binomial, RAF reference-allele frequency, SNP single-nucleotide polymorphism