AD and DP

EddieEddie Member
edited October 2012 in Ask the GATK team

Hello, I am wondering why in my resultant vcf file, the total number of reads calling reference and alternate base does not equal the DP value in all cases. In some cases, the total number of reads calling the reference and alternate base (AD) is less than DP. I have marked duplicates using Picard, therefore I am wondering if the DP value contains duplicates? Typical differences would be DP=49, AD=35, 7. So, although there isn't a drastic difference, I am still curious as to what is being reported here. Thank you.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The DP value is calculated based on unfiltered reads, so that includes reads that are filtered out from the calling for various reasons (low mapping qual etc.). That probably explains the small differences you observe.

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