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


CONCLUSIONS
All these findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results.
Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA. shabbir5@vt.edu.
Mohammad Shabbir
MS
Hasan
Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA. xwwu@vt.edu.
Xiaowei
X
Wu
Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA. lqzhang@vt.edu.
Liqing
L
Zhang
D000465:Algorithms; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D016045:Human Genome Project; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software