I am using GATK version 3.3 (latest release) and following the best practice for variant calling. Steps i am using is
1. Run haplotye caller and get the gVCF file
2. Run GenotypeGVCF across the samples to the get the VCF file
The Question is about the Genotype calling.
Here is an example:
GVCF file looks like this for a particular position
chr1 14677 . G . . END=14677 GT:DP:GQ:MIN_DP:PL 0/0:9:0:9:0,0,203
VCF file looks like this after genotyping with multiple samples.
chr1 14677 . G A 76.56 PASS . . GT:AD:DP:GQ:PL 0/1:8,1:9:4:4,0,180
In GVCF file there was no support for the alternate allele, but VCF file shows that there are 1 read supporting the alternate call.
Thanks ! Saurabh