Problem with GATK pipeline, merging VCF and ped file.

Hi to all

I have just started using GATK and I have few question about some tools and about the general workflow.

I have 3 exome-seq data from a trio and I have to detect rare or private variants that segregate with the disease.

From the 3 aligned bam file I procedeed with the GATK pipeline (ADDgroupInfo, MarkDup, Realign, BQSR, Unified Genotyper and variant filtration) and I generated 3 VCF file.

As now I have to use the PhaseByTrasmission tool, should I merge the 3 VCF file?

Or it was better to merge the BAM file after adding the group info and proceed with the other analysis?

And should I create my .ped file,(I visited http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped, but I couln't understand how ped file is generated) based on the read group that I have assigned?

Thanks!!!