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  • lollysticky
    Junior Member
    • Aug 2010
    • 4

    #1

    VCF question regarding missing INFO or FORMAT fields

    A combination of two questions which I can't directly resolve from reading the v4.3 specifications. They're mostly hypothetical as most variants won't encounter this situation


    Question 1
    If there is no INFO information (so: column 8 in the VCF file) present for a given variant, is the column just empty or is it represented by '.' ? Not every variant needs to have the same INFO fields present, so this scenario seems plausible.

    Question 2
    If There is no FORMAT/GENOTYPE information (so: column 9 and 10 in the VCF file) present for a given variant, are both columns empty or represented by '.' ? Same as above: not every variant needs to have the same FORMAT fields present, so this scenario seems plausible.

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