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GT and AD

if my vcf indicates the GT is 1/1 and the AD=14,4: what does the 14,4 indicate?

14 reads of the ALT and 4 that were not???? or something else

thank you
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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal/erroneous results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

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  • manolismanolis Member ✭✭✭
    edited November 2019

    Hi,

    In the header (first lines) of your vcf file you can find all the explanations:

    ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

    Best

  • dgewingdgewing Member
    I am sorry for not creating a more concise and complete question; I hope you will give me a 2nd chance.

    I understand that the AD provides the "unfiltered" allele depth, i.e. the number of reads that support each of the reported alleles and that the GT field provides the genotype of the sample and that "0" is the REF allele and "1" represents the first ALT allele. (1/1 is a homozygous alternate sample--0/0 is a homozygous reference sample)

    My question was seeking understanding of the combination of the two pieces of "coupled" data: GT and AD

    If the sample is homozygous alternate (1/1) and the AD is 14,4;how do I interpret those 2 pieces of data when they are for the same "position" (on the same line or on the same record or for the same position)??

    Again I apoligize for not making my question clear, and
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