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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

GATK UnifiedGenotyper Missing AD value in genotype

I have been using GATK (v2.2) UnifiedGenotyper to generate VCFs.
I did a multisample realignment around indels which generated a multisample BAM of size ~500Gb. After looking at some of the SNP calls I decided to try removing duplicates. I used MarkDuplicates with "REMOVE_DUPLICATES=true" and although only 10% of reads were duplicates, the BAM reduced to ~75Gb. This did not seem to affect the depth of reads at a site more than the expected ~10% but now the AD field in the genotype columns is missing. ie GT:AD:GQ 0/1:.:30
When I run UnifiedGenotyper with the old BAM prior to MarkDuplicates the AD field is present.

I am currently running the MarkDuplicates on each sample prior to realignment - because I think this makes the most sense, but isn't clear why this should matter,

Any ideas on what is happening here?

Answers

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