DNA Germline WGS UMI
The DRAGEN recipe includes the recommended pipeline specific commands.
/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. SDD /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
# UMI
--umi-enable true
--umi-source STRING #Default='qname'
--umi-library-type STRING #e.g. random-duplex
--umi-min-supporting-reads 1 #Default=2
# 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
# HLA genotyper
--enable-hla true
# Targeted caller
--enable-targeted true #Targeted
# Star allele
--enable-star-allele true
# PGX
--enable-pgx true #PGX
# Short tandem repeats
--repeat-genotype-enable true
# Multi-Region Joint Detection (MRJD)
--enable-mrjd true
--mrjd-enable-high-sensitivity-mode 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.
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
--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.
UMI
--umi-source STRING
Specify the input type for the UMI sequence. Options: qname, fastq, bamtag.
--umi-library-type STRING
Set the batch option for different UMIs correction. Options: random-duplex, random-simplex, nonrandom-duplex.
--umi-nonrandom-whitelist $PATH
If UMI is nonrandom, either a whitelist or correction table is required. The whitelist includes a valid UMI sequence per line.
--umi-correction-table $PATH
If UMI is nonrandom, either a whitelist or correction table is required. The correction table defaults to the table used by TruSight Oncology: <INSTALL_PATH>/resources/umi/umi_correction_table.txt.gz.
--umi-min-supporting-reads INT
Specify the number of matching UMI inputs reads required to generate a consensus read. Any family with insufficient supporting reads is discarded. The default is 2.
--umi-metrics-interval-file $BED
Target region in BED format.
--umi-emit-multiplicity both
--umi-start-mask-length INT
Number of additional bases to ignore from start of read. The default is 0. To reduce FP optionally set to 1.
--umi-end-mask-length INT
Number of additional bases to ignore from end of read. The default is 0. To reduce FP optionally set to 3.
For more information see: UMI Options.
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
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
--cnv-enable-mosaic-calling true
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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