ALT Contig Hash Table Options
The following options control See ALT Contig Hash Tables for more information on building hash tables from a reference that contains ALT contigs.
| • | --ht-alt-liftover |
The --ht-alt-liftover option specifies the path to the liftover file to build an ALT-aware hash table. This option is required when building from a reference with ALT contigs. SAM liftover files for hg38DH and hg19 are provided in /opt/edico/liftover.
| • | --ht-alt-aware-validate |
When building hash tables from a reference that contains ALT-contigs, building with a liftover file is required. To disable this requirement, set the --ht-alt-aware-validate option to false.
| • | --ht-decoys |
DRAGEN automatically detects the use of hg19 and hg38 references and adds decoys to the hash table when they are not found in the FASTA file. Use the --ht-decoys option to specify the path to a decoys file. The default is /opt/edico/liftover/hs_decoys.fa.
| • | --ht-suppress-decoys |
Use the --ht-suppress-decoys option to suppress the use of the decoys file when building the hash table.
| • | ht-mask-bed |
Use the ht-mask-bed option to specify a custom BED file that contains the regions of ALT contigs to mask.
| • | ht-allow-mask-and-liftover |
Use the ht-allow-mask-and-liftover option to build a hash table with both mask and liftover files.
