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?
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
indiciesdirectory . 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