hla translation

Hi 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 >HLA00001 HLA-A*01:01:01:01.

But A*01:01 matches in many places. I would be happy if there is a way to go from A*01:01 to HLA00001

Is there a way to obtain this?

Thanks

[andras86]

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!

[Rashesh7]

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:

1. Is there a plan to update the backend HLA database? The latest release just recently came out. (3.33.0)
2. 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.

Thank you!