RNA WTS
The DRAGEN recipe includes the recommended pipeline specific commands.
/opt/dragen/$VERSION/bin/dragen #DRAGEN install path
--ref-dir $REF_DIR #path to DRAGEN pangenome 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/scRNA
--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 Splice Variants
--enable-rna-splice-variant true
# RNA Gene Fusions
--enable-rna-gene-fusion true Notes and additional options
Hashtable
For DRAGEN RNA/scRNA 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
--enable-map-align true
Optionally disable map & align (default=true).
--enable-map-align-output true
Optionally save the output BAM (default=false).
Duplicate Marking
--enable-duplicate-marking true
By default, DRAGEN marks duplicate reads and exclude them from variant calling.
RNA Variant Calling
--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
--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 Splice
--rna-splice-variant-normals $PATH
Optional setting list of normal splice variants that will be used filter false positive calls. The file should be a tab separated file with the following first four columns: (1) contig name, (2) first base of the splice junction (1-based), (3) last base of the splice junction (1-based), (4) strand (0: undefined, 1: +, 2: -).
--rna-splice-variant-regions $PATH
Target region bed file. Required for panels. The name of the region must be specified in the fourth column.
RNA Fusion
--rna-gf-enriched-regions $PATH
For panels, the list of enriched genes should be set, either as a list of genes or a list of regions in BED format.
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