Reference Hashtable

For the DRAGEN CNV pipeline, the hashtable must be generated with the --enable-cnv option set to true, in addition to any other options required by other pipelines. When --enable-cnv is true, dragen generates an additional k-mer uniqueness map that the CNV algorithm uses to counteract mapability biases. The k-mer uniqueness map file only needs to be generated once per reference hashtable and takes about 1.5 hours per whole human genome.

The reference hashtable is a pregenerated binary representation of the reference genome. For information on generating a hashtable, see Prepare a Reference Genome.

The following is an example of a command to generate a hashtable.

dragen \
--build-hash-table true \
--ht-reference <FASTA> \
--output-directory <OUTPUT> \
--enable-cnv true \
--enable-rna true