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. 2015 Aug 19;9(1):20.
doi: 10.1186/s40246-015-0042-2.

Performance evaluation of indel calling tools using real short-read data

Mohammad Shabbir Hasan  1 , Xiaowei Wu  2 , Liqing Zhang  3
Affiliations

Performance evaluation of indel calling tools using real short-read data

Mohammad Shabbir Hasan et al. Hum Genomics. .

Abstract

Background: Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, many indel calling tools have been developed; however, evaluation and comparison of these tools using large-scale real data are still scant. Here we evaluated seven popular and publicly available indel calling tools, GATK Unified Genotyper, VarScan, Pindel, SAMtools, Dindel, GTAK HaplotypeCaller, and Platypus, using 78 human genome low-coverage data from the 1000 Genomes project.

Results: Comparing indels called by these tools with a known set of indels, we found that Platypus outperforms other tools. In addition, a high percentage of known indels still remain undetected and the number of common indels called by all seven tools is very low.

Conclusion: All these findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results.

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Figures

Fig. 1
Fig. 1
Categories of indel calling tools. Here ref is the reference sequence and actual is the observed sequence. (Partially taken from Abel and Duncavage [40])
Fig. 2
Fig. 2
Example of identical indels taking place in relative positions. (Adapted from Krawitz et al. [20])
Fig. 3
Fig. 3
Number of indels called by the seven tools for the 78 humans
Fig. 4
Fig. 4
Relationship between coverage and the pooled number of indels by the seven tools
Fig. 5
Fig. 5
Percentage of the gold standard indels called by the tools
Fig. 6
Fig. 6
Average F-measure for each tool for different lengths of indels
Fig. 7
Fig. 7
Average false-negative rate for each tool for different lengths of indels
Fig. 8
Fig. 8
Jaccard index for each pair of tools for each sample
Fig. 9
Fig. 9
Hierarchical clustering of the tools
See this image and copyright information in PMC

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