The Scientific and Technological Research Council of Turkey (TÜBITAK), Gebze, Kocaeli 41470, Turkey.
Bioinformatics. 2017 Nov 1;33(21):3468-3470. doi: 10.1093/bioinformatics/btx422.
The decreasing cost in high-throughput technologies led to a number of sequencing projects consisting of thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyse exome files are not adequate for larger VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Memory efficiency and avoiding computationally costly pre-processing step enable to carry out the analysis to be performed with ordinary computers. VCF-Explorer provides an easy to use environment where users can define various types of queries based on variant and sample genotype level annotations. VCF-Explorer can be run in different environments and computational platforms ranging from a standard laptop to a high performance server.
VCF-Explorer is freely available at: http://vcfexplorer.sourceforge.net/.
Supplementary data are available at Bioinformatics online.
高通量技术成本的降低导致了许多由数千个全基因组组成的测序项目。从外显子组到全基因组的范式转变带来了输出文件大小的显著增加。大多数为分析外显子组文件而开发的现有工具对于全基因组研究产生的较大 VCF 文件来说并不足够。在这项工作中，我们提出了 VCF-Explorer，这是一种能够处理大型文件的变体分析软件。内存效率和避免计算成本高的预处理步骤使得能够在普通计算机上执行分析。VCF-Explorer 提供了一个易于使用的环境，用户可以根据变体和样本基因型级别的注释定义各种类型的查询。VCF-Explorer 可以在不同的环境和计算平台上运行，范围从标准笔记本电脑到高性能服务器。
VCF-Explorer 可在以下网址免费获得：http://vcfexplorer.sourceforge.net/。
补充数据可在 Bioinformatics 在线获得。
