# RNA WTS

The DRAGEN recipe includes the recommended pipeline specific commands. A DRAGEN recipe is a predefined set of analysis parameters and workflow settings tailored for a specific type of genomic analysis. Some default parameters are included for clarity and are marked with comments.

```
  
/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 
```

## Notes and additional options

### Hashtable

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

See: [Product Files](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html)

### 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'. |


---

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