Compatibility of CHM13v2.0-aligned BAM with --graph PRG_MHC_GRCh38_withIMGT in HLA*LA

[dyfyf]

Dear HLA*LA developers,

Thank you for your excellent work on this tool. I have a question regarding reference genome compatibility.

I would like to run HLA-LA.pl using BAM files that were aligned to the CHM13v2.0 reference genome. Is it possible to use these BAM files as input while still specifying --graph PRG_MHC_GRCh38_withIMGT? Or does this graph require that the input BAM must also be aligned to GRCh38?

If CHM13v2.0-aligned BAMs are not compatible with the GRCh38 graph, would it be necessary to build a new graph corresponding to CHM13 (e.g., PRG_MHC_CHM13_withIMGT)?

Any clarification would be greatly appreciated.

Best wishes！