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VCF files: DP and AD fields definition: confilicting information

newbie16newbie16 Member
edited August 2012 in Ask the GATK team

Hello,
I am a bit confused with the definition of DP field in the vcf file generated by UnifiedGenotyper. The following page:
"http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html"
says that DP is "Total (unfiltered) depth over all samples." which implies that DP is number of NOT-FILTERED reads at a given locus.
However in the detailed text, it says "The DP field describe the total depth of reads that passed the Unified Genotypers internal quality control metrics". This implies that DP is number of FILTERED reads at a given locus.

Could you please clarify this? Also could you clarify if AD is for filtered or unfiltered reads.

Thanks

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    You are completely right - the documentation is incorrect and misleading. I'm going to fix the docs so that the corrected text gets pushed out tonight with the GATK 2.1 release. If you check again tomorrow it should make more sense!

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