superFreq
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Published
20 hours ago •
ChristofferFlensburg
ChristofferFlensburg
NNNN as ref allele
Hi Christoffer,
Another bug:
| chr | start | end | reference | variant | inGene | severity | effect |
|---|---|---|---|---|---|---|---|
| 1 | 40150191 | 40150196 | NNNNNN | - | HPCAL4 | 10 | inframe_deletion |
Same data as in the previous github issue.
All the best,
Gil
hey!
The reported reference NNNN in deletions is a known issue that I probably won't fix soon. Essentially I set things up in a stupid way only accounting for SNVs, and including indels wasn't a big deal, apart from this reference information missing... That entire thing would need rewriting, but I think it's low reward per effort. So you'll have to deal with the NNN reference entries for now, sorry. I guess most people don't really care what bases are lost (maybe the VEP annotation will tell you which amino acids are lost in a later column?), and if you really care you can check in IGV.
