Fig 9. Indel calling results of GATK HaplotypeCaller and VarScan with the whole exome sequencing data of GIAB HG002.

(a) The indel calling results of GATK HaplotypeCaller and (b) VarScan. The evaluation results of true positive (TP), false positive (FP), and false negative (FN) of indel calls were generated using hap.py. The numbers on top of each bar show the total number of indels in this category. The indels in STR regions and not in STR regions are marked with different colors.