Giters

FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

How to output the result with 8 digits ?

lidd77 opened this issue · comments

commented

HI,
Whether Optitype supports the output of 8 digits ?
I checked the paper ,but not found any information about it .

Thanks .

commented

The direct output of Optitype is an HLA-ID corresponding to a fully specified HLA allele.

Just return the results dataframe in line 416 of OptitypePipeline.py.

However, I would advise against using 8-digit results here since Optitype uses only exons 2 and 3 and thus is unable to resolve correctly 8-digit genotypes if the synonymous mutation does not lie within exons 2 and 3.