ALT-Aware Hash Tables

To enable ALT-aware mapping in DRAGEN, build GRch38 (and other references with ALT contigs) with a liftover file by using the --ht-alt-liftover option. The hash table builder classifies each reference sequence as primary or alternate based on the liftover file, and packs primaries before alternates in reference.bin. SAM liftover files for hg38DH and hg19 are in the /opt/edico/liftover folder. The --ht-alt-liftover option specifies the path to the liftover file to build an ALT-aware hash table.

To override the liftover file requirement, set the --ht-alt-aware-validate option to false when building the hash tables and when running dragen.