I was given some vcfs from Illumina, and I'm trying to understand what was used to call the variants. For each individual, there are "Poly" and "MAXGT" calls.
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The specifications are spelled out in Illumina's BaseSpace software, information found here: http://supportres.illumina.com/docum..._15044182a.pdf
"The sample column gives the values specified in the FORMAT column. One MAXGT sample column is provided for the normal genotyping (assuming the reference). For reference, a second column is provided for genotyping assuming the site is polymorphic. See the Starling documentation for more details."
Looks like it's similar in spirit to GATK's Discovery mode vs. Genotype Given Alleles (though I'm not sure if they provide allelic options).
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