I'm running the haplotype caller grouping my samples in batches to reduce the time it takes, but I'd like to be able to use VQSR on all the samples together.
Is it possible to merge the vcf files and run VQSR on all the samples together?
No, unfortunately VQSR will only work on samples that were called together. We are working on a workaround for this, but it will take another 6 to 8 weeks before it is ready for public release.
If you think about it it makes sense as the annotations are statistics computed per site, not per sample and it's not always easy to combine them in meaningful way.