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

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 undet

SUBMITTER: Hasan MS 

PROVIDER: S-EPMC4545535 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature