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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:
From the same site in 68148-2.g.vcf
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!