Are variants outside genes dropped from the output?

[Paururo]

Some of my variants fall between annotated genes. I cannot tell from the output
whether they are being reported and I am missing them, or whether get_MNV only
keeps what lands inside a feature.

Does it drop them?

[Paururo]

No. A variant that falls outside every feature in your annotation is still
reported, as a row of its own:

Column	What it says
Gene	intergenic
AA Changes	-
SO Term	intergenic_variant
Impact	MODIFIER

So an intergenic variant is an answer, not a silence. The amino acid column is
- because there is no codon to translate, not because something went wrong.

If you would rather not see them, --exclude-intergenic removes them.

Worth knowing separately: a variant inside a gene can also come back with -
in the amino acid column, when no codon can be built for it. That is also a
reported row, not a dropped one.