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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data

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Is it based on hg38 genome?

xiasijian opened this issue · comments

commented

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

commented

Same problem！If you have the answer？

commented

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!

commented

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.