Fig. 2

Fraction of all, true and false variants called by a different number of variant callers in case of simulated data. Sequencing reads covering the exonic region of a selected chromosome were simulated for 50 artificially generated samples with pre-known variations to the human genome (i.e. reference variants). Variants were called on the BWA–MEM and Bowtie 2 aligned reads by HaplotypeCaller, UnifiedGenotyper, FreeBayes and SAMtools. Stacked bars with different colors represent the fraction of all (a), true (b) and false (c) variants with respect to the reference variants, called by a given number of variant callers at various coverage depths (see the common legend on the bottom). Each panel is divided into four subpanels, where the top pair represents: SNPs, bottom pair: indels, left column: BWA alignment, right-column: Bowtie 2 alignment