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Add "intergenic" consequence

Open holtgrewe opened this issue 1 year ago • 1 comments

Is your feature request related to a problem? Please describe. We currently annotate variants on transcripts, intronic, upstream, and downstream. However, we don't annotate intergenic variants.

Describe the solution you'd like Annotate intergenic variants as such intergenic_variant.

Describe alternatives you've considered N/A

Additional context

  • http://www.sequenceontology.org/miso/current_svn/term/SO:0001628

holtgrewe avatar Jul 17 '24 08:07 holtgrewe

The SO term is available and annotated only if there are no overlapping transcripts found, see https://github.com/varfish-org/mehari/blob/bfd396b279393ffc2569424e58c322d9a135e5df/src/annotate/seqvars/csq.rs#L197-L222

tedil avatar Jan 03 '25 10:01 tedil