Hello,
We're preparing VCFs for public release. Our working VCF has a considerable amount of both info and format field annotations and also filters in both. We also have another header lines, such as the GATKCommand, which should be removed. I'd like to prepare a minimal VCF that strips all information except a minimal whitelist of annotations. A handful of GATK tools have options to help here. SelectVariants will allow me to exclude filtered (site-level filters), but this doesnt clean up filtered genotypes (even if genotypes are set to no call). It appears I could run VariantAnnotator with --excludeAnnotation; however, I think I would need to apply a blacklist (i.e. need to target each one to remove), as opposed to a whitelist of those to keep, which would be a little more robust. I could probably make a simple walker that does this, but if existing tools can be combined to do this I'd prefer not to. Are there existing features that could help, specifically with stripping out annotations and filters from INFO and FORMAT fields?
Thanks,
Ben