RNA Panel

The DRAGEN recipe includes the recommended pipeline specific commands.

  
/opt/dragen/$VERSION/bin/dragen         #DRAGEN install path 
--ref-dir $REF_DIR                      #path to DRAGEN graph hashtable 
--output-directory $OUTPUT 
--intermediate-results-dir $PATH        #e.g. SDD /staging 
--output-file-prefix $PREFIX 
# Inputs 
--fastq-list $PATH                      #see 'Input Options' for FQ, BAM or CRAM 
--fastq-list-sample-id $STRING 
# Mapper 
--enable-rna true 
--annotation-file $GTF                  #GTF or GFF3 format 
--enable-map-align true                 #required for RNA 
--enable-map-align-output true          #optionally save the output BAM 
--enable-sort true                      #default=true 
--enable-duplicate-marking true         #default=true 
# Small variant caller 
--enable-variant-caller true 
--vc-target-bed $VC_TARGET_BED 
# RNA Quantification 
--enable-rna-quantification true 
--rna-library-type A                    #see 'RNA Quant' 
--rna-quantification-gc-bias true 
# RNA Gene Fusions 
--enable-rna-gene-fusion true 
--rna-gf-enriched-regions $PATH         #see 'RNA Fusion' 

Notes and additional options

Hashtable

For DRAGEN RNA runs, it is recommended to use the linear hashtable.

See: Product Files

Input options

DRAGEN input sources include: fastq list, fastq, bam, or cram.

FQ list Input

--fastq-list $PATH 
--fastq-list-sample-id $STRING 

FQ Input

--fastq-file1 $PATH 
--fastq-file2 $PATH 
--RGSM $STRING 
--RGID $STRING 

BAM Input

--bam-input $PATH 

CRAM Input

--cram-input $PATH 

Mapping and Aligning

Option	Description
--enable-map-align true	Optionally disable map & align (default=true).
--enable-map-align-output true	Optionally save the output BAM (default=false).

Duplicate Marking

Option	Description
--enable-duplicate-marking true	By default, DRAGEN marks duplicate reads and exclude them from variant calling.

RNA Variant Calling

Option	Description
--vc-target-bed $PATH	Restrict the variants called to a target bed. For WTS, a bed file specifying the gene-coding regions should be provided to avoid calling erroneous variants in non-coding regions due to noisy reads.

RNA Quant

Option	Description
--rna-library-type	Set the library according to the read orientations. Set to 'A' to auto detect the correct read orientation. Alternatively select 'IU', 'ISR', 'ISF', 'U', 'SR', or 'SF'.

RNA Amplicon

To enable RNA amplicon, set:

• --enable-rna-amplicon true, and

• --amplicon-target-bed $PATH.

If RNA amplicon mode is enabled and the amplicon bed file already includes the gene name, then it is not required to set the ENRICH options option, since DRAGEN will read the enriched genes names from the amplicon BED file (fifth column).