VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data

Abstract

Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.

Figure 1.

VCF.Filter overview and workflow for interactive prioritization of genetic variants. VCF.filter takes a VCF file as input, implements several filtering and analysis methods, and produces a filtered VCF file as output. The user can optionally provide additional input files for customized filtering, such as lists of genomic regions to include or exclude, and a table of allele frequencies in a reference cohort. VCF.Filter also produces a visualization of genetic variants using the Hilbert curve and tables of cohort allele frequencies for variant filtering.

Figure 2.

Analysis example using the ‘Filter variants’ module of VCF.Filter. Once a VCF file has been loaded into VCF.Filter, the user can interactively define filtering rules, for example to identify disease-linked variants. Filtering can be based on annotations in the VCF file (e.g. variant type, location, or variant effect predictions). In addition, the user can upload a table of variant allele frequencies in a suitable reference cohort and filter potentially disease-linked variants by cohort allele frequencies. Furthermore, lists of genomic regions for inclusion (pass) and exclusion (non-pass) can be configured to restrict the analysis to certain genomic regions and/or to specifically exclude other regions. This screenshot shows an example with filtering on one standard VCF field (CHROM) and on three custom VCF annotations. The output is written to the text area in the bottom part of the user interface and can also be saved to a VCF file.