Building the HLA-Specific Reference Subdirectory
An HLA-specific reference subdirectory can be built by executing
dragen \
--build-hash-table true \
--ht-build-hla-hashtable=true \
--output-directory={REF-DIR}
This command will create anchored_hla as a subdirectory of the target {REF-DIR} supplied as an argument to --output-directory as above.
The HLA-specific reference subdirectory can be built at the same time as the primary reference construction. An example command-line for this mode is
dragen \
--build-hash-table true \
--ht-build-hla-hashtable=true \
--output-directory={REF-DIR} \
--ht-reference {PATH-TO}primary_reference.fasta