How to add Custom VCF Data for HLA Typing with HISAT-genotype

[allen890205]

HI,

I am currently working on integrating Taiwanese-specific variants from a VCF file (TW1492.vcf) into the HISAT-genotype tool for HLA typing. My objective is to observe if including the variants from the TW1492.vcf file affects the HLA typing results compared to the default graph typing results.

I have explored the indicies directory . However, I am unsure how to proceed with adding my VCF data to the HISAT-genotype graph for consideration during HLA typing.

Could you guide me on how to incorporate the TW1492.vcf data into the HISAT-genotype workflow? Is there a specific script or command that I should use to update the reference graph with my VCF data?

Thank you for your assistance.

Best regards,
Allen,Wu