Hi,

I'd like to annotate a set of variants I called by other methods outside R and BioC. After looking into some tutorials, I lean towards locateVariants function within the VariantAnnotation package. However, I've seen its second argument must be a TxDb object, which is intended for transcripts, and not any genomic region (is this correct???). If I am interested n variants lying on any region of the genome (transcripts or not), shouldn't I use other method? If I unterstood wrong and TxDb objects contain all regions of the genome, then the problem would be solved.

Thanks

Where do you get the idea that the second argument must be a TxDb? From ?locateVariants:

subject: A TxDb or 'GRangesList' object that serves as the annotation.
          GFF files can be converted to TxDb objects with
          'makeTxDbFromGFF()' in the 'GenomicFeatures' package.

locateVariants is intended to tell you how your variants relate to anything on a genome that can be defined in a GRangesList, which could be transcripts, but it could also be anything else, depending on what you are trying to do.