# DRAGEN v4.4.6 T/N Recipe
The following DRAGEN recipes are specific for Illumina FFPE DNA Prep with Exome 2.5 Enrichment **tumor and normal libraries** (do not use for [tumor only](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/tumor-only-analysis) analysis or for a different library prep method). A general recipe for Somatic analysis of Tumor Normal samples with UMI is provided on [DRAGEN v4.4 support pages](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi).
```bash
/opt/dragen/$VERSION/bin/dragen #DRAGEN install path
--ref-dir $REF_DIR #path to DRAGEN linear hashtable
--output-directory $OUTPUT
--intermediate-results-dir /staging #tmp dir on fast SDD
--output-file-prefix $PREFIX
# Inputs
--tumor-fastq-list $PATH #see 'Input Options' for FQ, BAM or CRAM
--tumor-fastq-list-sample-id $STRING
--fastq-list $PATH #see 'Input Options' for FQ, BAM or CRAM
--fastq-list-sample-id $STRING
# Mapper
--enable-map-align true
--enable-map-align-output true #save the output BAM (default=false)
--qc-coverage-ignore-overlaps true #do not double-count overlapping mates
# UMI
--umi-enable true
--umi-library-type nonrandom-duplex
--umi-min-supporting-reads 1
--umi-start-mask-length 1
--umi-end-mask-length 3
--tumor-normal-has-umi both
# Small variant caller
--enable-variant-caller true
--vc-target-bed $VC_TARGET_BED #see Resource Files page
--vc-systematic-noise $PATH #see Resource Files page
--vc-enable-umi-solid true
--vc-sq-call-threshold 3
--vc-sq-filter-threshold 15
--vc-enable-non-primary-allelic-filter true
--vc-enable-triallelic-filter false
--vc-skip-germline-tagging true
# CNV
--enable-cnv true
--cnv-use-somatic-vc-baf true
--cnv-target-bed $VC_TARGET_BED
--cnv-combined-counts $PATH #see Resource Files page
# Annotation #annotation is required if enabling TMB
--enable-variant-annotation true
--variant-annotation-data $PATH #see notes below
--variant-annotation-assembly GRCh37/8
# TMB
--enable-tmb true
# HRD Scoring
--enable-hrd true #requires CNV
# Microsatellite Instability (MSI)
--msi-command tumor-only
--max-base-quality 63 #default if UMI is enabled
--msi-coverage-threshold 40 #see notes below
--msi-microsatellites-file ${microsatellite_file} #see Resource Files page
--msi-ref-normal-dir ${normal_reference_directory} #see Resource Files page
```
## Notes and additional options
### Hashtable
For DRAGEN somatic runs it is recommended to use the linear (non-graph) hashtable.
Please see: [DRAGEN references](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html)
### Inputs
[Here are support pages for the formats of different input file types](https://support-docs.illumina.com/SW/DRAGEN_v39/Content/SW/DRAGEN/Inputfiles_fDG.htm).
FQ list Input
```
--fastq-list $PATH
--fastq-list-sample-id $STRING
```
or
```
--tumor-fastq-list $PATH
--tumor-fastq-list-sample-id $STRING
```
FQ Input
```
--fastq-file1 $PATH
--fastq-file2 $PATH
--RGSM $STRING
--RGID $STRING
```
or
```
--tumor-fastq1 $PATH
--tumor-fastq2 $PATH
--RGSM-tumor $STRING
--RGID-tumor $STRING
```
BAM Input
```
--bam-input $PATH
```
or
```
--tumor-bam-input $PATH
```
CRAM Input
```
--cram-input $PATH
```
or
```
--tumor-cram-input $PATH
```
### Mapper
Option
Description
--qc-coverage-ignore-overlaps true
resolve all of the alignments for each fragment and avoid double-counting any overlapping bases
### UMI
The above recipe details UMI options specific for the Illumina FFPE DNA Prep with Exome 2.5 Enrichment Library kit.
### SNV
The `vc-sq-filter-threshold` flag can be used to fine-tune the "somatic quality" value at which variants are called in order to balance sensitivity and specificity. Variants with values between the `vc-sq-call-threshold` and `vc-sq-filter-threshold` values are labeled as "weak\_evidence" in the output VCF file. The [default SQ Filter threshold in DRAGEN](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi) for tumor-normal analysis is 17.5.
### Annotation
Top directory containing Nirvana data file. Instructions on how to download the resource are at . DRAGEN is expecting a top directory containing the sub-directories Cache, References, Supplementary Annotation.
### Microsatellite Instability (MSI)
Microsatellite Instability (MSI) is run in tumor-only mode, but other variants and biomarkers are calculated in tumor-normal mode. msi-coverage-threshold is a required parameter for both tumor-only and tumor-normal, and should be set according to the sample coverage. The sites in the msi-microsatellites-file need to match those in the dist files within the msi-ref-normal-dir .
---
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