DNA Germline WGS
The DRAGEN recipe includes the recommended pipeline specific commands.
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.
FQ list Input
FQ Input
BAM Input
CRAM Input
Mapping and Aligning
--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
--enable-duplicate-marking true
By default, DRAGEN marks duplicate reads and exclude them from variant calling.
SNV
DRAGEN SNV VC employs machine learning based variant recalibration (DRAGEN-ML). It processes read and other contextual evidence to remove false positives, recover false negatives and reduce zygosity errors. No additional setup is required. DRAGEN-ML is enabled by default as needed, when running the germline SNV VC on hg19 or hg38.
Note that we do not recommend changing the default QUAL thresholds of 3 for DRAGEN-ML and 10 for DRAGEN without ML. These values differ from each other because DRAGEN-ML improves the calibration of QUAL scores, leading to a change in the scoring range.
--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)
--vc-emit-ref-confidence GVCF
To enable gVCF output.
--vc-enable-vcf-output
To enable VCF file output during a gVCF run, set to true. The default value is false.
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
VNTR
--sv-vntr-merge false
Option to disable automatic merging of VNTR calls into SV VCF.
For more details see: VNTR Calling
HLA
--enable-hla
Enable HLA typer (this setting by default will only genotype class 1 genes)
--hla-as-filter-min-threshold
Internal option to set min alignment score threshold. The default is 59 and works for WES and WGS. Set to 29 for panels.
--hla-as-filter-ratio-threshold
Minimum Alignment score of a read mate to be considered. The default is 0.67 and works for WES and WES. Set to 0.85 for panels.
--hla-enable-class-2
Extend genotyping to HLA class 2 genes (default=true).
CNV
--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
If you are using somatic targeted panels with a set of genes supplied with the capture kit, then you can bypass segmentation by specifying a cnv-segmentation-bed and using cnv-segmentation-mode=bed.
--cnv-population-b-allele-vcf $POP_VCF
--cnv-enable-cyto-output true
Enable Cytogenetics-compatible output (default true), see Cytogenetics Modality. Only available with the Germline ASCN caller.
--cnv-enable-mosaic-calling true
Enable MOSAIC-calling mode (default true). Only available with the Germline ASCN caller.
For more information, see CNV Calling.
# Multi-Region Joint Detection (MRJD)
--enable-mrjd
If set to true, MRJD is enabled for the DRAGEN pipeline.
--mrjd-enable-high-sensitivity-mode
If set to true, MRJD high sensitivity mode is enabled for the DRAGEN pipeline. See the MRJD section in the user guide for information on variant types reported in MRJD default mode and high-sensitivity mode (default=false).
For futher details refer to MRJD.
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