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