# Illumina TruPath Genome WGS

A DRAGEN recipe, like this one, is a predefined set of analysis parameters and workflow settings tailored to a specific type of genomic analysis. For clarity, some default parameters are explicitly included and annotated with comments.

```
  
/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. SSD /staging 
--output-file-prefix $PREFIX 
# Inputs 
--fastq-list $PATH                      #see 'Input Options' 
--fastq-list-sample-id $STRING 
# Illumina TruPath Genome 
--enable-proximity true 
# Mapper 
--enable-map-align true                 #optional with BAM/CRAM input 
--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-phasing-min-fragments 0 
# SV 
--enable-sv true 
# CNV 
--enable-cnv true 
--cnv-enable-self-normalization true 
# Targeted caller 
--enable-targeted true 
# Short tandem repeats 
--repeat-genotype-enable true 
# Multi-Region Joint Detection (MRJD) 
--enable-mrjd true 
```

## Notes and additional options

### Hashtable

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

### Input options

TruPath Genome Prep only supports fastq list and fastq input. For BCL input, first create FASTQs using [BCL conversion](https://help.connected.illumina.com/dragen/product-guides/dragen-v4.5/bcl-conversion).

FQ list Input

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

FQ Input

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