Think about storing Variants with "N" sequences
Open
- Dominant language
- Python
- Stars
- 30
- Forks
- 3
- Avg merge
- 9h 28m
- Merged PRs (30d)
- 42
Description
Currently we reject: `chr5 123456 AG GNAT`
With: "non-standard bases in ALT sequence"
I am not sure what to do in this case. In some ways, it's worth storing. But the annotation is going to be sparse/bad, and if someone else uploads the same variant in effect, but with the base filled in, then we won't have matched/linked them, and eg a common variant (and tag/classification etc) will be missed
I guess we don't have that now, as we reject it
Should probably see what VEP does with it. And liftover etc etc
Also, we could just display a warning on the variant page if it contains an N
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.