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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data
BSD 3-Clause "New" or "Revised" License
180 stars 74 forks source link

Is it based on hg38 genome? #135

Closed xiasijian closed 2 months ago

xiasijian commented 1 year ago

image Thanks for your excellent software, I want to know whether these software is based on hg38 genome.

edceeyuchen commented 1 year ago

Same problem！If you have the answer？

kiranfranklin999 commented 2 months ago

Same doubt! Could anyone confirm this? I'm using bam files aligned to hg38 and wanted to know whether this software is compatible with hg38 genome.

Thank you!

b-schubert commented 2 months ago

No, it uses a custom reference of all known HLA sequences. But you can use your alignments to prefilter for reads falling into the HLA superlocus, which will speed up optitype‘s inference.