Abnormally high per-sample depth after running GenotypeGVCFs

I first posted this question as a reply to something related (see https://gatkforums.broadinstitute.org/gatk/discussion/7318/what-is-the-significance-of-depth-across-all-samples-dp-in-info#latest) but realized it might not get visibility there.

After running GenotypeGVCFs, I'm seeing that the per-sample depth (DP in FORMAT) reported is consistently much higher than the sample depths reported in the original gvcfs. For example:

From the vcf file, looking at sample 68148-2:
GT:AD:DP:GQ:PGT:PID:PL 0/0:522,0:522:0:.:.:0,0,13060

From the same site in 68148-2.g.vcf
GT:DP:GQ:MIN_DP:PL 0/0:13:36:12:0,36,376

As you can see, the depth in the vcf file is WAY higher. This is found for all samples at this site, and at a glance seems to be occurring at most of the sites in the vcf. Why might the depth scores be so inflated after genotypegvcfs?

I don't know if this helps, but I checked a vcf produced from genotypegvcfs on a subset of my population, and I see that the same inflated depths are being reported. I also get the same result using GATK versions 3.7 and 3.8.

Thank you for your help!

Answers

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