Add optional gvcf file to vtools-evaluate
vtools-evaluate uses compares two VCF files. However, the typical use case is to compare a set of known variants (for example from an OpenArray) to the variants found using NGS sequencing. In this context, the known variants can contain sites that are either:
- called as homref in the g.vcf file
- are missing completely from the NGS data
These two cases should not be treated the same (as 'missing data'). When a g.vcf file is specified, the homref calls in this file can be matched against the calls in the OpenArray file.