DISCOVAR now generates variant lists using the Variant Calling Format (VCF). This is the standard used by the community and is supported by many tools. Whilst the VCF file contains all events found by DISCOVAR, the complementary
.variant file may contain additional information not easily represented in the VCF format. We encourage our users to look at both. The VCF should be filtered prior to use, and we have provided a tool and instructions on how to do this.
To facilitate calling variants using DISCOVAR on large genomes, we have created a tool to merge VCF files generated for overlapping regions. Simply run DISCOVAR on each region in turn (or in parallel to speed things up), then merge the VCF files that are produced. We currently recommend using a 50 kb region size, with a 10 kb overlap.
For more information on the VCF output, filtering and merging, please refer to our manual.