I am a newbie at WES and Trios.

I have run some uBAMs from Mum, Dad, Child through ExomeGermlineSingleSample_v3.1.7.

I now want to end up with a 'best pratice' vcf for the trio. I came across this article:

https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinement-workflow-for-germline-short-variants

I want to clarify that:

a) this is the 'best practice' and

b) do we end up with recalibrated variants from VQSR at the end of the exome workflow (I cannot find this information)

If not, is it best to run the following on the single sample g.vcfs (output from ExomeGermlineSingleSample_v3.1.7)

1) consolidate GVCFs into a GenomicsDB datatore run joint genotyping

(https://gatk.broadinstitute.org/hc/en-us/articles/360035889971--How-to-Consolidate-GVCFs-for-joint-calling-with-GenotypeGVCFs)

2) Build a recalibration model

https://gatk.broadinstitute.org/hc/en-us/articles/360037262291-VariantRecalibrator

3) apply VQSR filtering 

https://gatk.broadinstitute.org/hc/en-us/articles/360036485072-ApplyVQSR

4) Then run the following:

https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinement-workflow-for-germline-short-variants