The annotations appear in the order in which the checkboxes are checked. This is confusing because the user would expect the annotations to appear in the same order as the checkboxes appear in the dialog to select them.
Also, the order that the 'Variant Annotations' and 'Genotype Annotations' checkboxes appear seems to be the order of the variant header 'INFO' records. For 'Genotype Annotations' this is probably okay since these are a fixed order. But for the 'Variant Annotations' (from the INFO field in the vcf record), the ordering seems a bit more random — many of the fields appear in alphabetical order, but not all of the fields. For example, in the demo dataset, the INFO field 'culprit' is followed by an uppercase 'OLD_MULTIALLELIC'. So it is better to order these alphabetically, case sensitive.
The annotations appear in the order in which the checkboxes are checked. This is confusing because the user would expect the annotations to appear in the same order as the checkboxes appear in the dialog to select them.
Also, the order that the 'Variant Annotations' and 'Genotype Annotations' checkboxes appear seems to be the order of the variant header 'INFO' records. For 'Genotype Annotations' this is probably okay since these are a fixed order. But for the 'Variant Annotations' (from the INFO field in the vcf record), the ordering seems a bit more random — many of the fields appear in alphabetical order, but not all of the fields. For example, in the demo dataset, the INFO field 'culprit' is followed by an uppercase 'OLD_MULTIALLELIC'. So it is better to order these alphabetically, case sensitive.