Fig. 3

Comparison of Canary with BWA, GATK and VarDict. Graph showing the number of true positive (TP) variants (expected = 46) for three pipelines run against six Acrometrix control samples containing known variants at a certified allele frequency (left hand axis). The three pipelines were; Canary performing read alignment and variant calling (blue bars), BWA-MEM 2 performing read alignment and GATK haplotype caller for variant calling (red bars) and BWA-MEM 2 performing read alignment and VarDict for variant calling (green bars). The mean variant allele frequency for each of the pipeline variants is shown as coloured diamonds and the control sample expected frequency is shown as black diamonds (right hand axis). Raw data and statistics are available in Additional file 2: Table S1