ALT-Contigs
The following options control See References with ALT Contigs for more information on building hash tables from a reference that contains ALT contigs.
| • | --ht-mask-bed: Set a custom BED file to be used to define which regions to mask instead of the default file. BED files for hg38DH and hg19 are provided in /opt/edico/fasta_mask. |
| • | --ht-alt-liftover: Set a liftover file to build a liftover based ALT-aware hash table. SAM liftover files for hg38DH and hg19 are provided in /opt/edico/liftover. |
| • | --ht-allow-mask-and-liftover: Allows you to use --ht-mask-bed and --ht-alt-liftover together. |
