9 months ago by
The first option Sequence changes (SNPs, MNPs, InDels) on the SnpEff tool is where the
VCF input dataset is selected.
The second option on the tool form Input format is where
VCF datatype is specified.
BEDdata can be input instead of
VCF, and selected as the input format, but annotating BED datasets is a deprecated function (as noted in the second option's choices) and might now work as expected.
The message you report is tool form help to alert about mismatches in the inputs/parameters before a job is submitted. To avoid this, check to see if you have one type of input selected for the first option and if the datatype is a mismatch for the second option. The input dataset (VCF or BED) should have that datatype assigned and be a match for the datatype specification.
Thanks! Jen, Galaxy