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Table 1 Optimised F1 scores in A. thaliana (Cvi-0). In comparison to the reference SNPs obtained from 1001 genomes consortium data, scores are derived when using real WGS and WGBS data, alongside in silico WGBS data derived from the WGS reads and alignments, respectively

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

  Real data in silico
  WGS WGBS reads alignments
GATK3.8 0.9189 0.8177 0.8508 0.9069
Freebayes 0.8247 0.7670 0.8039 0.8247
Platypus (default) 0.7423 0.7026 0.7709 0.7935
Platypus (assembly) 0.6378 0.5980 0.6449 0.6509