Hi all, 
I have two objectives for my analysis: 

1. To find out denovo and rare variants from autism trios analysis `Trios: (Father, Mother, Proband)`
2. To detect frequently occuring mutation across autism patient.

I have used GATK best practice to identify the germline variants across 15 trios (`Total 45 samples [15X3]`) and I have generated `gVCF` file for all the 45 samples.

Can some one guide me how to call `de novo variants` from this trios cohort?

run GATK VariantAnnotator with  '-A PossibleDeNovo --pedigree the.ped ' 