Recommend tools for joint-calling from multiple vcf files after "vg call"

[shin0727]

Hello,
First, thank you for providing such a great tool for variant analysis.

I used "vg pack" and "vg call" to generate VCF files for 31 cattle. However, for a population study, I need to merge the VCF files from each individual into one. Specifically, I want to perform joint calling to identify common variants.

The documentation recommends using the GLnexus tool for joint calling after DeepVariant. Is there a joint calling tool that can be used after vg call?

[glennhickey]

That's a great question, but I am unfortunately not aware of any specif joint calling tools for vg call.