Tumor-only analysis

The performance of the Illumina FFPE DNA Prep with Exome 2.5 Enrichment kit with tumor only samples is currently being evaluated. The DRAGEN v4.4 user guide provides a recipe for DNA Somatic Tumor-Only Solid WES UMI workflow. Settings specific for this kit are included here.

/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
--validate-pangenome-reference false   #currently the linear reference is recommended for somatic analysis
# UMI
--umi-enable true 
--umi-library-type nonrandom-duplex
--umi-min-supporting-reads 1
--umi-start-mask-length 1
--umi-end-mask-length 3
# 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-enable-germline-tagging true 
--vc-enable-non-primary-allelic-filter true
--vc-enable-triallelic-filter false       
# CNV 
--enable-cnv true
--cnv-population-b-allele-vcf $POP_SNPs  #Path to population SNP VCF; see https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-preprocessing#b-allele-counts-ascn-callers
--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
--tmb-enable-proxi-filter 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                              
--msi-microsatellites-file ${microsatellite_file}        #see Resource Files page
--msi-ref-normal-dir ${normal_reference_directory}       #see Resource Files page