hla translationSee original GitHub issue
For some downstream analysis I need to identify the fasta sequence used for the hla allele called.
For instance, if optitype called
A*01:01 I would need to know its fasta sequence, which would be
A*01:01 matches in many places. I would be happy if there is a way to go from
Is there a way to obtain this?
- Created 5 years ago
- Comments:6 (3 by maintainers)
Top GitHub Comments
Hi Rashesh, I know the next major release (handling Class II, somatic calling and a fresh database) is becoming a running joke by now, but it’s coming. I’m glad to hear that you found OptiType robust across technologies!
Hi Andras, Thank you for the quick reply. That makes sense. If we need the full allele name I can edit OptiTypePipeline.py as you mentioned above.
Last couple of questions:
- Is there a plan to update the backend HLA database? The latest release just recently came out. (3.33.0)
- Is there a plan to add Somatic variant calling?
I apologize for many questions. Its just I recently benchmarked a few tools and found OptiType to be more robust across technologies and with good accuracy. And it would be great to have a somatic calling capability.