VCF was created by the 1000 Genomes Project as a way to store genome variations and has since become the de facto standard in human genomics. Handling VCF files, however, is not always straightforward. Although a VCF file can be opened and viewed in any text editor, browsing or searching whole genome VCF files is often slow and clumsy. Command-line tools designed to handle VCF files are faster, but are hard to use for non-bioinformaticians. Given the popularity of the VCF format, the genomics community is in need for an ultra-fast yet easy-to-use tool to browse, search, split and combine VCFs.
With Differ, Diploid delivers such a tool to the community, free of charge.
Opening a 1.5 GB VCF file in a text editor can take a while, even on modern computers. Differ opens these VCFs in a second or two on any modern Mac*. You’ll notice the difference.
No more 0/1
Differ presents variants in a table instead of showing them in plain text. Inspect the selected variant in a separate pane and see major properties at a glance. No more translating 0/1 either, Differ does the work for you and shows the corresponding alleles.
The fastest way to search a VCF is through command-line tools, but to most geneticists using these tools feels like eating glass. Differ searches VCF files by dividing the search task over all available processor cores, allowing you to search VCFs faster than any bioinformatics guru - no Terminal required.
If your VCF has been annotated with SnpEff, Differ shows the SnpEff annotations in a separate table, allowing you to search variants by gene name or effect.
Focussing on a specific chromosome, gene or any other subset of variants? You can easily export variants of interest to Excel, Numbers or VCF.
Split VCFs in a split second
Need only specific samples in a multiplex VCF file? Simply select the samples you’re interested in and export them to separate files.
Until now, combining two VCFs into one was even harder than printing them and gluing them together. With Differ, you can combine two VCF files exactly the way you want.