haplotye Caller

Hi

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 0/0:99:0,0,203

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