Pipeline Specific Hash Tables

When building a hash table, DRAGEN configures the options for DNA analysis by default. To run RNA-Seq data, you must build an RNA-Seq hash table by setting --ht-build-rna-hashtable to true. If running RNA-Seq alignment, use the original --output-directory instead of the automatically generated subdirectory.

If using the CNV pipeline, set --enable-cnv to true. The command generates an additional Kmer hash map that is used in the CNV algorithm. Illumina recommends to always use the --enable-cnv option, so you can perform CNV calling with the same hash table used for mapping and aligning.

To run the methylation pipeline, you must build a methylation-specific hash table. DRAGEN can build a single-pass or legacy multipass methylation hash table. Methylation runs using a single-pass hash table are completed faster than the legacy multipass hash tables. Single-pass hash tables are recommended for building methylation tables and running analyses.

Hash Table Type

Hash Table Commands

single-pass
• --ht-methylated-combined=true
• --ht-seed-len 27

multipass
• --ht-methylated=true
• --ht-seed-len 27
• --ht-max-seed-freq 16

The following is an example of a single-pass hash table build. The example generates a combined hash table in your reference index folder under the methyl_converted subdirectory.

dragen --build-hash-table true \ --output-directory $REFDIR \ --ht-reference $FASTA \ --ht-num-threads 40 \ --ht-methylated-combined=true \ --ht-seed-len 27

Methylation runs require building two special hash tables with reference bases converted from C to T in one table and G to A in the other table. The conversions are performed automatically when using the --ht-methylated command line option. The converted hash tables are generated in two subdirectories under the folder specified using the --output-directory command line option. The subdirectories are named CT_converted and GA_converted, corresponding with the base conversions. When using the hash tables for methylated alignment runs, make sure to refer to the --output-directory folder, not the subdirectories.

The base conversions remove a significant amount of information from the hash tables. You might need to use different hash table parameters than in a conventional hash table build. The following options are recommended for building hash tables for mammalian species.

dragen --build-hash-table=true --output-directory $REFDIR --ht-reference $FASTA --ht-max-seed-freq 16 --ht-seed-len 27 --ht-num-threads 40 --ht-methylated=true