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Fig. 4 | BMC Genomics

Fig. 4

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

Fig. 4

The shared fraction of true and false positive variants in real and simulated data for A. thaliana (Cvi-0), following analysis with GATK UnifiedGenotyper. Distinct WGBS datasets were simulated from both the real WGS alignments and the real WGS reads, separately. The panels denote A true positives, before and B after filtering, according to recommended hard-filter thresholds in GATK best-practices, and C false positives, also before and D after filtering. The thresholds chosen for filtering are further described in Supplementary Table S3

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