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.

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--ht-mask-bed: Set a custom BED file that defines which regions to mask. If not provided, the DRAGEN software automatically applies BED files for hg38 and hg19 from /opt/edico/fasta_mask.

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--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.

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--ht-allow-mask-and-liftover: Allows you to use --ht-mask-bed and --ht-alt-liftover together.

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--ht-suppress-mask: Suppress automatic detection of the default mask bed files when building the hash table.