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Akgün M, Demirci H. VCF-Explorer: filtering and analysing whole genome VCF files. Bioinformatics. 2017;33(21):3468-3470doi: 10.1093/bioinformatics/btx422.
Akgün, M., & Demirci, H. (2017). VCF-Explorer: filtering and analysing whole genome VCF files. Bioinformatics (Oxford, England), 33(21), 3468-3470. https://doi.org/10.1093/bioinformatics/btx422
Akgün, Mete, and Demirci, Hüseyin. "VCF-Explorer: filtering and analysing whole genome VCF files." Bioinformatics (Oxford, England) vol. 33,21 (2017): 3468-3470. doi: https://doi.org/10.1093/bioinformatics/btx422
Akgün M, Demirci H. VCF-Explorer: filtering and analysing whole genome VCF files. Bioinformatics. 2017 Nov 01;33(21):3468-3470. doi: 10.1093/bioinformatics/btx422. PMID: 29036499.
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Bioinformatics. 2017 Nov 01;33(21):3468-3470. doi: 10.1093/bioinformatics/btx422.

VCF-Explorer: filtering and analysing whole genome VCF files.

Bioinformatics (Oxford, England)

Mete Akgün, Hüseyin Demirci

Affiliations

  1. The Scientific and Technological Research Council of Turkey (TÜBITAK), Gebze, Kocaeli 41470, Turkey.

PMID: 29036499 DOI: 10.1093/bioinformatics/btx422

Abstract

SUMMARY: 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.

AVAILABILITY AND IMPLEMENTATION: VCF-Explorer is freely available at: http://vcfexplorer.sourceforge.net/.

CONTACT: [email protected].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: [email protected]

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