5 Base DNA Germline 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' for FQ, BAM or CRAM 
--fastq-list-sample-id $STRING 
# 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 
# 5-Base 
--methylation-conversion illumina 
--methylation-generate-cytosine-report true 
--methylation-compress-cx-report true 
# Small variant caller 
--enable-variant-caller true 
# Annotation 
--variant-annotation-data $NIRVANA_PATH 
--enable-variant-annotation true 
# SV 
--enable-sv true 
# CNV 
--enable-cnv true 
--cnv-enable-self-normalization true 

Notes and additional options

Hashtable

For DRAGEN germline runs, it is recommended to use the pangenome hashtable.

See: Product Files

Input options

DRAGEN input sources include: fastq list, fastq, bam, or cram. For BCL input, first create FASTQs using 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 

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).
--Aligner.clip-pe-overhang 2	Clean up any unwanted UMI indexes. Only use when reads contain UMIs, but UMI collapsing was not run.

Duplicate Marking

Option	Description
--enable-duplicate-marking true	By default, DRAGEN marks duplicate reads and exclude them from variant calling.

5-Base Methylation

Option	Description
--methylation-conversion STRING	Library conversion for methylation analysis. Options: none, c_t, mc_t, illumina (default=none).
--methylation-protocol STRING	Library protocol for methylation analysis. Options: none, directional, non-directional, directional-complement, pbat. The default value for methylation-conversion=illumina is directional, otherwise it is none.
--methylation-mapq-threshold INT	Only reads with MAPQ greater or equal than the threshold will be included in methyl-seq analysis (default=0).
--methylation-generate-mbias-report true	Whether to generate a per-sequencer-cycle methylation bias report (default=true).
--mbias-report-include-overlaps	Calculate methylation stats for overlapping bases between mates (default=false).
--methylation-generate-cytosine-report true	Whether to generate a genome-wide cytosine methylation CX_report file (default=false).
--methylation-compress-cx-report true	Set to true to enable compression of the CX_report (default=true).
--methylation-keep-ref-cytosine true	Set to true to keep all reference cytosines in the CX_report file, even if they don't appear in the input reads (default=false).
--enable-cpg-methylated-mapping true	Enable methylated mapping with base conversions restricted to CpG context (default=true). When false, runs DRAGEN Methylation 3-base map/align instead.
--methylation-report-to-vcf	Specify methylation type (none, cg, or c) which is reported in VCF files (default=c).
--methylation-report-to-vcf	Specify methylation type (none, cg, or c) which is reported in gVCF files (default=cg).

For more information see: 5-Base Pipeline.

SNV

Option	Description
--vc-target-bed	Limit variant calling to region of interest.
--vc-combine-phased-variants-distance INT	Maximum distance in base pairs (BP) over which phased variants will be combined. Set to 0 to disable. Valid range is [0; 15] BP (Default=2)

Annotation

For instructions on how to download the Nirvana annotation database, please refer to Nirvana

CNV

Option	Description
--cnv-enable-gcbias-correction true	Enable or disable GC bias correction when generating target counts.
--cnv-segmentation-mode $SEG_MODE	Option to override the default segmentation algorithm. Defaults include slm for germline WGS, aslm for somatic WGS, and hslm for targeted analysis.
--cnv-segmentation-bed $PATH	Specify a segmentation bed file to add pre-defined segments to be called.