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The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R’s built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.

Software type:
Command line interface
Restrictions to use:
Operating system:
Unix/Linux, Mac OS, Windows
Programming languages:
GNU General Public License version 2.0
Computer skills:
WhopGenome version 0.9.2
R (≥ 1.8.0)
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  • Ulrich Wittelsbuerger <ulrich.wittelsbuerger at uni-duesseldorf.de>


Institute for Computer Science, Heinrich Heine University, D-40255 Düsseldorf, Germany

Funding source(s)

This work was supported by the German Research Foundation [DFG grants EXC 1028 and CRC 680].

  • (Wittelsburger et al., 2015) WhopGenome: high-speed access to whole-genome variation and sequence data in R. Bioinformatics.
    PMID: 25273104
  • Animals
    • Homo sapiens

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