Fig. 1
From: Evaluation of variant calling tools for large plant genome re-sequencing
Experimental design. A raw read set in fastq (raw) and two preprocessed sets by quality trimming (trim) and duplicate removal (rep1) are shown in the first row of rectangles. Each set was aligned to the wheat reference genome v1.0 by one of two mapping tools (mappers): BWA-mem or Bowtie2. The mapped bam files were used for variant calling using seven variant tools (callers). A total of 42 combinations/experiments were evaluated for two mapping tools and seven variant calling tools (callers) using three data preprocess types by criteria: Mapping, Concordance, Discordance and Receiver Operating Characteristic (ROC). The final settings were applied to a large population data set