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 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-gvcf	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)

For more detail on the small variant caller in somatic mode please refer to Somatic Mode

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.

For more information, see CNV Calling.