Generation of allsites vcf from joint-genotyped samples

[echille]

Hello!

I am trying to run a tool, pixy that requires the use of an AllSites VCF (a VCF that contains all invariant sites in addition to variant sites). I've tried following the Best practices for multi-sample variant calling with DeepVariant workflow, but it seems that it does not support this functionality. Do you have any suggestions on how to generate the AllSites VCF using GLnexus? Or could this potentially be added as a future feature?

Thanks!