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Figure 4 | BMC Research Notes

Figure 4

From: Comparison of insertion/deletion calling algorithms on human next-generation sequencing data

Figure 4

Validation of indels called by Pindel (A,B), GATK-UG (C,D), and GATK-HC (E, F) in targeted exon sequencing with whole exome sequencing, and whole exome sequencing with whole genome sequencing using uniform parameter settings across the targets. HaplotypeCaller performed the most reliably across the different targets. Pindel indel calls had the lowest validation rates when settings were unchanged across the targets. Lower TES validation rates in all three tools suggest either more false positives due to high depth of coverage in TES or insufficient depth or coverage in WES to validate the TES calls.

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