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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?


Issue Analytics

  • State:open
  • Created 5 years ago
  • Reactions:1
  • Comments:6 (3 by maintainers)

github_iconTop GitHub Comments

andras86commented, Aug 24, 2018

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!

Rashesh7commented, Aug 24, 2018

Hi Andras, Thank you for the quick reply. That makes sense. If we need the full allele name I can edit 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!

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