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GATK UnifiedGenotyper Missing AD value in genotype

rwnessrwness Member Posts: 20

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,371 admin

    The difference in size between the files suggests you may have had a processing issue that messed up your files. I would recommend starting from scratch with your original files. While you're at it you should consider also updating your version of GATK.

    Geraldine Van der Auwera, PhD

  • JVJAIJVJAI Member Posts: 5

    What are the reasons why the AD field would be missing from a UG run? Does it work in the GENOTYPE_GIVEN_ALLELES mode?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,371 admin

    In the original post it sounds like the AD annotation was removed when the Picard tool was run, not that it was omitted from the UG run.

    Geraldine Van der Auwera, PhD

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