[gatk 3.6.0] GVCF - haplotypecaller - cross referencing multiple VCF

Question

[Agamemnon]

Hi there,

how do you make a GVCF file from bam files, using [gatk 3.6] haplotypecaller if wanting to compare patient with their two parents?

I have three vcf files, but no gvcf files. I would like to be able to compare de novo as well as inherited variants. Are there any alternative processes apart from using GATK [3.6.0] GenotypeGVCF, followed by SelectVariants and then running the annotation software/database?

Thanks

Aga