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Fig. 3 | BMC Genomics

Fig. 3

From: Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches

Fig. 3

ROC-like comparisons in real and simulated data. In response to an increasing variant quality (QUAL) threshold, SNPs derived from real WGS data are compared to those derived from equivalent WGBS data after in silico bisulfite conversion of either reads or alignments, followed by preprocessing with the double-masking procedure, in A. thaliana (Cvi-0). The real WGBS dataset from Figure 2A is also displayed alongside in each panel for comparison. Panels show results from conventional software A Freebayes, B GATK3.8 and C Platypus (default mode). True and false positives are evaluated based on both the substitution context and the estimated genotype

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BMC Genomics

ISSN: 1471-2164

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