HLA coordinates disagree with 3730 results
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Because the exon boundaries don't line up with the codon boundaries, the actual start of exon2 is not reported as position 1, and we don't report the last basepair of exon2. There are probably similar problems with exon3.
We need some way to deal with the partial codons at the end of the exons.
One possible solution would be to use only the complete codons in the coordinate reference, then configure some extra nucleotides to report at either end.
We'd have to test what happens when the first or last complete codon has a variant. Would it report a deletion instead of a substitution?
Gen asked about this, because she's trying to summarize the HLA results and compare them to the 3730 results.
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Research direction
No files or tests are named. Trace how HLA exon coordinates are built and compared with 3730 results, focusing on partial codons at the ends of exon2 and exon3 and variants in the first or last complete codon. Done means the reported coordinates include the relevant exon bases and variant classifications are verified against 3730 results.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100