Joint Genotyping Recommendation

[SophieS9]

I'm running DeepVariant Pepper on various samples from different trios. I need to carry out joint genotyping as I need to be aware of when a variant is homozygous reference and when there is poor confidence in a region so the variant couldn't be determined.

I've tried using GLNexus but there appears to be an issue with the format of the gVCF from pepper - see issue dnanexus-rnd/GLnexus#287

Are there any recommendations for different joint genotyping approaches?

Thanks!

Sophie