I've used the Unified Genotyper for variant calling with GATK version 2.5.2. This was the info for a private variant.
However, after select variants to exclude non variant and variants not passing Filter, the AD changed and eliminated the alternative reads though the DP remained unchanged.
I think I recall another post having a similar issue due to multithreaded use of select variants
APologies for not commenting on this post instead as I had already posted this prior to seeing the other post!
I've seen related issues discussed here but not exactly this one. I'm following closely the current recommendations for an exome pipeline, and the GATK version,downloaded from git, was v2.5-2-gf57256b, Compiled 2013/06/06 17:28:57.
For example, I have two samples with heterozygous variants 12:81503433C>G. The AD values for the the samples in the raw vcf file, and the SNVs-only file were 15,14 and 20,15 for the two samples and these agree with what I see in IGV. There was nothing in the indels-only file at that position. The AD values were the same in the recalibrated SNVs-only file. But after combining the recalibrated SNVs and indels with CombineVariants the AD values inexplicably became 21,0 and 0,24 respectively. This seems to be happening to many variants.