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Location of variant in multi-sample calling

esbeneickhardtesbeneickhardt DenmarkMember
edited January 2015 in Ask the GATK team

Dear Ensembl

While using your best practices pipeline, using multisample calling, I get these multi-allelic variants. As I am interested in the precise position of certain variants, I would like to know if there is a way to identify, where a variant is located. This is ofcause possible in most cases, but I have a subset of my variants, where I cannot see how this can be done

Examples from my VCF-file:



In the first example, I cannot see which "T" has been deleted - this could be any of them:



In the second example, I cannot see which "A" has been deleted:



Is there any way, I can get information on which one it is?

Esben Eickhardt


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited January 2015


    Hi Esben,

    There is no way to know for certain, biologically, which nucleotide is "missing". In effect, it does not matter because the result is the same either way. The way we deal with this is we use conventions such as left-aligning, which basically says that anytime this case occurs, we consider that it is the leftmost base that is the deleted one.


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