Command Line Options

This section provides information on all the DRAGEN command-line options, including the name used in the configuration file, the command-line equivalent, a description, and the range of values.

NOTE After upgrading to a new version of DRAGEN, it is recommended to first run with the default DRAGEN options, including all filtering options, and then add any specific filters only if needed.

General Software Options

The following options are in the default section of the configuration file. The default section is at the top of the configuration file and does not have a section name (eg, [Aligner]) associated with it. Some mandatory fields must be specified on the command line and are not present in configuration files.

Name	Description	Command Line Equivalent	Range
append-read-index-to-name	By default, DRAGEN names both mate ends of pairs the same. When set to true, DRAGEN appends /1 and /2 to the two ends.	--append-read-index-to-name	true/false
aws-s3-region	Specifies the geographical region of AWS S3 buckets.	--aws-3-region
bam-input	Specifies aligned BAM file for input to the DRAGEN variant caller.	-b, --bam-input
bam-list	Specifies CSV file that contains a list of BAM files to process.	--bam-list
bcl-conversion-only	Performs Illumina BCL conversion to FASTQ format.	--bcl-conversion-only	true/false
bcl-input-directory	Inputs BCL directory for BCL conversion.	--bcl-input-directory
bcl-only-lane	For BCL input, the option converts only specified lane number. By default, all lanes are converted.	--bcl-only-lane	1–8
sample-sheet	For BCL input, the option sets the path to SampleSheet.csv file. The default location is the BCL root directory.	--sample-sheet
strict-mode	For BCL input, the option cancels analysis if any files are missing. The default value is false by default.	--strict-mode	true/false
first-tile-only	Converts only the first tile of each lane during BCL conversion. Use for testing or debugging.	--first-tile-only	true/false
run-info	Sets the path to RunInfo.xml file. The default is <flow cell>/RunInfo.xml.	--run-info
bcl-sampleproject-subdirectories	For BCL conversion, the option outputs to subdirectories based on sample sheet Sample_Project column.	--bcl-sampleproject-subdirectories
no-lane-splitting	Disables splitting output FASTQ files by lane. The default value is false.	--no-lane-splitting	true/false
bcl-only-matched-reads	Specifies if unmapped reads are output to files marked as Undetermined. The default value is false.	bcl-only-matched-reads	true/false
bcl-use-hw	If set to false, the option prevents DRAGEN FPGA acceleration during BCL conversion. The default value is true.	--bcl-use-hw	true/false
bcl-num-parallel-tiles	Specifies the number of tiles to process in parallel. The default value is dynamically determined.	--bcl-num-parallel-tiles	1-
bcl-num-conversion-threads	Specifies the number of conversion threads per tile. The default value is dynamically determined.	--bcl-num-conversion-threads	1-
bcl-num-compression-threads	Specifies the number of CPU threads for output fastq.gz compression. The default value is dynamically determined.	--bcl-num-compression-threads	1-
bcl-num-decompression-threads	Specifies the number of CPU threads for BCL input decompression. The default value is dynamically determined.	--bcl-num-decompression-threads	1-
shared-thread-odirect-output	Uses alternative shared-thread ODIRECT file output. The default value is false.	--shared-thread-odirect-output	true/false
build-hash-table	Generates a reference hash table.	--build-hash-table	true/false
cram-input	Specifies the CRAM file input for the variant caller.	--cram-input
cram-list	Specifies CSV file that contains a list of CRAM files to process.	--cram-list
dbsnp	Sets the path to the variant annotation database VCF (or *.vcf.gz) file.	--dbsnp
enable-auto-multifile	Imports subsequent segments of the *_001.{dbam,fastq} files.	--enable-auto-multifile	true/false
enable-bam-indexing	Enables generation of a BAI index file.	--enable-bam-indexing	true/false
enable-cram-indexing	Enables generation of a CRAI index file.	--enable-cram-indexing	true/false
enable-cnv	Enables copy number variant (CNV).	--enable-cnv	true/false
enable-duplicate-marking	Enables the flagging of duplicate output alignment records.	--enable-duplicate-marking	true/false
enable-map-align-output	Enables saving the output from the map/align stage. If only running map/align, the default value is true. If running the variant caller, the default value is false.	--enable-map-align-output	true/false
enable-methylation-calling	Automatically adds tags related to methylation and outputs a single BAM for methylation protocols.	--enable-methylation-calling	true/false
enable-sampling	Automatically detects paired-end parameters by running a sample through the mapper/aligner.	--enable-sampling	true/false
enable-sort	Enables sorting after mapping/alignment.	--enable-sort	true/false
enable-variant-caller	Enables the variant caller.(default=false)	--enable-variant-caller	true/false
enable-variant-deduplication	Enables variant deduplication. The default value is false.	--enable-variant-deduplication	true/false
enable-vcf-compression	Enables compression of VCF output files. The default value is true.	--enable-vcf-compression	true/false
enable-vcf-indexing	Outputs a *.tbi index file in addition to the output VCF/gVCF. The default is true.	--enable-vcf-indexing	true/false
fastq-file1	Specifies FASTQ file to input to the DRAGEN pipeline. Gzipped format can be used.	-1, --fastq-file1
fastq-file2	Specifies second FASTQ file with paired-end reads to input.	-2, --fastq-file2
fastq-list	Specifies CSV file that contains a list of FASTQ files to process.	--fastq-list
fastq-list-sample-id	If the RGSM entry matches the given Sample ID parameter for fastq-list.csv input, the option processes the entry.	--fastq-list-sample-id
fastq-list-all-samples	If true, process all samples in the fastq-list file, even when there are multiple RGSM (Sample ID) values.	--fastq-list-all-samples	true/false
fastq-n-quality	Specifies the base call quality to output for N bases. Automatically added to fastq-n-quality for all output N bases.	--fastq-n-quality	0–255
fastq-offset	Sets the FASTQ quality offset value.	--fastq-offset	33 64
filter-flags-from-output	Filters output alignments with any bits set in val present in the flags field. Hex and decimal values accepted.	--filter-flags-from-output
force	Forces overwrite of existing output file.	-f
force-load-reference	Forces loading of the reference and hash tables before starting the DRAGEN pipeline.	-l
generate-md-tags	Generates MD tags with alignment output records. The default value is false.	--generate-md-tags	true/false
generate-sa-tags	Generates SA:Z tags for records that have chimeric or supplemental alignments.	--generate-sa-tags	true/false
generate-zs-tags	Generate ZS tags for alignment output records. The default value is false.	--generate-zs-tags	true/false
ht-alt-liftover	SAM format liftover file of alternate contigs in reference.	--ht-alt-liftover
ht-mask-bed	Specifies the BED file for base masking.	--ht-mask-bed
ht-allow-mask-and-liftover	Allows the hash table builder to run with both ht-alt-liftover and ht-mask-bed. Default is false.	--ht-allow-mask-and-liftover	true/false
ht-build-rna-hashtable	Enables generation of RNA hash table. The default value is false.	--ht-build-rna-hashtable	true/false
ht-cost-coeff-seed-freq	Sets cost coefficient of extended seed frequency.	--ht-cost-coeff-seed-freq
ht-cost-coeff-seed-len	Sets cost coefficient of extended seed length.	--ht-cost-coeff-seed-len
ht-cost-penalty-incr	Sets cost penalty to incrementally extend a seed another step.	--ht-cost-penalty-incr
ht-cost-penalty	Sets cost penalty to extend a seed by any number of bases.	--ht-cost-penalty
ht-decoys	Specifies the path to a decoys file.	--ht-decoys
ht-max-dec-factor	Sets the maximum decimation factor for seed thinning.	--ht-max-dec-factor
ht-max-ext-incr	Sets the maximum bases to extend a seed by in one step.	--ht-max-ext-incr
ht-max-ext-seed-len	Specifies the maximum extended seed length.	-- ht-max-ext-seed-len
ht-max-seed-freq	Sets the maximum allowed frequency for a seed match after extension attempts.	--ht-max-seed-freq	1–256
ht-max-table-chunks	Specifies the maximum ~1 GB thread table chunks in memory at one time.	--ht-max-table-chunks
ht-mem-limit	Specifies the memory limit (hash table + reference) in units (KB, MB, GB).	--ht-mem-limit
ht-methylated	Automatically generates C->T and G->A converted reference hash tables.	--ht-methylated	true/false
ht-num-threads	Sets maximum worker CPU threads for building hash table.	--ht-num-threads
ht-rand-hit-extend	Includes a random hit with each EXTEND record of the frequency record.	--ht-rand-hit-extend
ht-rand-hit-hifreq	Includes a random hit with each HIFREQ record.	--ht-rand-hit-hifreq
ht-ref-seed-interval	Specifies the number of positions per reference seed.	--ht-ref-seed-interval
ht-reference	References file in FASTA format to build a hash table.	--ht-reference
ht-seed-len	Sets initial seed length to store in hash table.	--ht-seed-len
ht-size	Specifies the size of hash table in units (KB, MB, GB).	--ht-size
ht-soft-seed-freq-cap	Specifies the soft seed frequency cap for thinning.	--ht-soft-seed-freq-cap
ht-suppress-decoys	Suppresses the use of a decoys file when building a hash table.	--ht-suppress-decoys
ht-target-seed-freq	Sets the target seed frequency for seed extension.	--ht-target-seed-freq
input-qname-suffix-delimiter	Controls the delimiter used for append-read-index-to-name and for detecting matching pair names with BAM input.	--input-qname-suffix-delimiter	/ :
interleaved	Specifies the interleaved paired-end reads in single FASTQ.	-i
intermediate-results-dir	Specifies directory to store intermediate results in (eg, sort partitions).	--intermediate-results-dir
lic-no-print	Suppresses the license status message at the end of a run.	--lic-no-print	true/false
lic-server	Specifies the license server for cloud sites: http://<base64_use>:<base64_password>@	--lic-server
lic-instance-id-location	Use this option to override the default cloud instance ID location	--lic-instance-id-location
lic-credentials	Path to license credentials file that specifies the license credentials and domain.	--lic-credentials
methylation-generate-cytosine-report	Generates a genome-wide cytosine methylation report.	--methylation-generate-cytosine-report	true/false
methylation-generate-mbias-report	Generates a per system cycle methylation bias report.	--methylation-generate-mbias-report	true/false
methylation-TAPS	If input assays are generated by TAPS, the option is set to true.	--methylation-TAPS	true/false
methylation-match-bismark	If true, the option matches bismark tags exactly, including bugs.	--methylation-match-bismark	true/false
methylation-protocol	Describes library protocol for methylation analysis.	--methylation-protocol	none directional nondirectional directional-complement
num-threads	Specifies the number of processor threads to use.	-n, --num-threads
output-directory	Specifies the output directory.	--output-directory
output-file-prefix	Outputs file name prefix to use for all files generated by the pipeline.	--output-file-prefix
output-format	Sets the format of the output file from the map/align stage. The following values are valid:BAM (the default),CRAM (lossless), SAM, or DBAM (a proprietary binary format)	--output-format	BAM/ CRAM/ SAM / DBAM
pair-by-name	Shuffles the order of BAM input records so paired-end mates are processed together.	--pair-by-name
pair-suffix-delimiter	Changes the delimiter character for suffixes.	--pair-suffix-delimiter	/ . :
preserve-bqsr-tags	Determines whether to preserve BI and BD flags from the input BAM file, which can cause problems with hard clipping.	--preserve-bqsr-tags	true/false
preserve-map-align-order	Produces output file that preserves original order of reads in the input file.	--preserve-map-align-order	true/false
qc-coverage-region-1	Generates coverage region report using bed file 1.	--qc-coverage-region-1
qc-coverage-region-2	Generates coverage region report using bed file 2.	--qc-coverage-region-2
qc-coverage-region-3	Generates coverage region report using bed file 3.	--qc-coverage-region-3
qc-coverage-reports-1	Describes the types of reports requested for qc-coverage-region-1.	--qc-coverage-reports-1	full_res/cov_report
qc-coverage-reports-2	Describes the types of reports requested for qc-coverage-region-2.	--qc-coverage-reports-2	full_res/cov_report
qc-coverage-reports-3	Describes the types of reports requested for qc-coverage-region-3.	--qc-coverage-reports-3	full_res/cov_report
qc-coverage-region-1-thresholds	Declares the thresholds to use in cov_report for qc-coverage-region-1.	--qc-coverage-region-1-thresholds	List of up to 11 numbers separated by commas
qc-coverage-region-2-thresholds	Declares the thresholds to use in cov_report for qc-coverage-region-2.	--qc-coverage-region-2-thresholds	List of up to 11 numbers separated by commas
qc-coverage-region-3-thresholds	Declares the thresholds to use in cov_report for qc-coverage-region-3.	--qc-coverage-region-3-thresholds	List of up to 11 numbers separated by commas
ref-dir	Specifies the directory containing the reference hash table. If the reference is not already loaded into the DRAGEN card, the option automatically loads the reference.	-r, --ref-dir
ref-sequence-filter	Outputs only reads mapping to the reference sequence.	--ref-sequence-filter
remove-duplicates	If true, the option removes duplicate alignment records instead of only flagging them.	true/false
RGCN	Specifies the read group sequencing center name.	--RGCN
RGCN-tumor	Specifies the read group sequencing center name for tumor input.	--RGCN-tumor
RGDS	Provides the read group description.	--RGDS
RGDS-tumor	Provides the read group description for tumor input.	--RGDS-tumor
RGDT	Specifies the read group run date.	--RGDT
RGDT-tumor	Specifies the read group run date for tumor input.	--RGDT-tumor
RGID	Specifies read group ID.	--RGID
RGID-tumor	Specifies read group ID for tumor input.	--RGID-tumor
RGLB	Specifies the read group library.	--RGLB
RGLB-tumor	Specifies the read group library for tumor input.	--RGLB-tumor
RGPI	Specifies the read group predicted insert size.	--RGPI
RGPI-tumor	Specifies the read group predicted insert size for tumor input.	--RGPI-tumor
RGPL	Specifies the read group sequencing technology.	--RGPL
RGPL-tumor	Specifies the read group sequencing technology for tumor input.	--RGPL-tumor
RGPU	Specifies the read group platform unit.	--RGPU
RGPU-tumor	Specifies read group platform unit for tumor input.	--RGPU-tumor
RGSM	Specifies read group sample name.	--RGSM
RGSM-tumor	Specifies read group sample name for tumor input.	--RGSM-tumor
sample-size	Specifies number of reads to sample when enable-sampling is true.	--sample-size
sample-sex	Specifies the sex of the sample.	--sample-sex
strip-input-qname-suffixes	Determines whether to strip read-index suffixes (eg, /1 and /2) from input QNAMEs. If set to false, the option preserves entire name.	--strip-input-qname-suffixes	true/false
tumor-bam-input	Specifies aligned BAM file for the DRAGEN variant caller in somatic mode.	--tumor-bam-input
tumor-bam-list	Specifies CSV file that contains a list of BAM files for the mapper, aligner, and somatic variant caller.	--tumor-bam-list
tumor-cram-input	Specifies aligned CRAM file for the DRAGEN variant caller in somatic mode.	--tumor-cram-input
tumor-cram-list	Specifies a CSV file that contains a list of CRAM files for the mapper, aligner, and somatic variant caller.	--tumor-cram-list
tumor-fastq-list	Inputs a CSV file containing a list of FASTQ files for the mapper, aligner, and somatic variant caller.	--tumor-fastq-list
tumor-fastq-list-sample-id	Specifies the sample ID for the list of FASTQ files specified by tumor-fastq-list.	--tumor-fastq-list-sample-id
tumor-fastq1	Inputs FASTQ file for the DRAGEN pipeline using the variant caller in somatic mode. The input file can be gzipped.	--tumor-fastq1
tumor-fastq2	Inputs second FASTQ file. Reads are paired to tumor-fastq1 reads for the DRAGEN pipeline using the variant caller in somatic mode. The input file can be gzipped.	--tumor-fastq2
vd-eh-vcf	Inputs the ExpansionHunter VCF file for variant deduplication. The input file can be gzipped.	--vd-eh-vcf
vd-output-match-log	Outputs a file that describes the variants that matched during deduplication. The default value is false.	--vd-output-match-log	true/false
vd-small-variant-vcf	Inputs small variant VCF file for variant deduplication. The input file can be gzipped.	--vd-small-variant-vcf
vd-sv-vcf	Inputs structural variant VCF for variant deduplication. The input file can be gzipped.	--vd-sv-vcf
verbose	Enables verbose output from DRAGEN.	-v
version	Prints the DRAGEN version, the Hash Table version and exits.	-V,--version

Mapper Options

The following options are in the [Mapper] section of the configuration file. For more detailed information on these options, see [DNA Mapping]{.underline}.

Name	Description	Command Line Equivalent	Range
ann-sj-max-indel	Specifies maximum indel length to expect near an annotated splice junction.	--Mapper.ann-sj-max-indel	0–63
edit-chain-limit	For edit-mode 1 or 2, the option sets maximum seed chain length in a read to qualify for seed editing.	--Mapper.edit-chain-limit	edit-chain-limit >= 0
edit-mode	Controls when seed editing is used. The following values represent the different edit modes: 0 is no edits, 1 is chain length test, 2 is paired chain length test, 3 is full seed edits	--Mapper.edit-mode	0–3
edit-read-len	For edit-mode 1 or 2, controls the read length for edit-seed-num seed editing positions.	--Mapper.edit-read-len	edit-read-len > 0
edit-seed-num	For edit-mode 1 or 2, controls the requested number of seeds per read to allow editing on.	--Mapper.edit-seed-num	edit-seed-num >= 0
enable-map-align	Enable the mapper/aligner (Default=true)	--enable-map-align	true/false
map-orientations	Restricts the orientation of read mapping to only forward in the reference genome or only reverse-complemented. The following values represent the different orientations (paired end requires normal):0 is normal (paired-end inputs must use normal), 1 is reverse-complemented, 2 is no forward	--Mapper.map-orientations	0–2
max-intron-bases	Specifies maximum intron length reported.	--Mapper.max-intron-bases
min-intron-bases	Specifies minimum reference deletion length reported as an intron.	--Mapper.min-intron-bases
seed-density	Controls requested density of seeds from reads queried in the hash table	--Mapper.seed-density	0 > seed-density > 1

Aligner Options

The following options are in the [Aligner] section of the configuration file. For more information, see [DNA Aligning]{.underline}

Name	Description	Command Line Equivalent	Value
aln-min-score	A signed integer that specifies a minimum acceptable alignment score to report the baseline for MAPQ. When using local alignments (global is 0), aln-min-score is computed by the host software as 22 * match-score. When using global alignments (global is 1), aln-min-score is set to -1000000. Host software computation can be overridden by setting aln-min-score in configuration file.	--Aligner.aln-min-score	−2,147,483,648 to 2,147,483,647
clip-pe-overhang	When nonzero, clips 3' read ends overhanging their mate's 5' ends as aligned. Set 1 to soft-clip overhang, 2 to hard-clip.	--Aligner.clip-pe-overhang	0–2
dedup-min-qual	Specifies a minimum base quality for calculating read quality metric for deduplication.	--Aligner.dedup-min-qual	0–63
en-alt-hap-aln	Allows haplotype alignments to be output as supplementary.	--Aligner.en-alt-hap-aln	0–1
en-chimeric-aln	Allows chimeric alignments to be output as supplementary.	--Aligner.en-chimeric-aln	0–1
gap-ext-pen	Specifies the penalty for extending a gap.	--Aligner.gap-ext-pen	0–15
gap-open-pen	Specifies the penalty for opening a gap (ie, insertion or deletion).	gap-open-pen	0–127
global	Controls whether alignment is end-to-end in the read. The following values represent the different alignments: 0 is local alignment (Smith-Waterman) 1 is global alignment (Needleman-Wunsch)	--Aligner.global	0–1
hard-clips	Specifies alignments for hard clipping. The following values represent the different alignments: Bit 0 is primary Bit 1 is supplementary Bit 2 is secondary	--Aligner.hard-clips	3 bits
map-orientations	Constrains orientations to accept forward-only, reverse-complement only, or any alignments. The following values represent the different orientations: 0 is any 1 is forward only 2 is reverse only	--Aligner.map-orientations	0–2
mapq-max	Specifies ceiling on reported MAPQ. The default value is 60.	--Aligner.mapq-max	0–255
mapq-strict-js	Specific to RNA. When set to 0, a higher MAPQ value is returned, expressing confidence that the alignment is at least partially correct. When set to 1, a lower MAPQ value is returned, expressing the splice junction ambiguity.	--mapq-strict-js	0–1
match-n-score	A signed integer that specifies the score increment for matching where a read or reference base is N.	--Aligner.match-n-score	-16–15
match-score	Specifies the score increment for matching reference nucleotide.	--Aligner.match-score	When global = 0, match-score > 0 When global = 1, match-score >= 0
max-rescues	Specifies maximum rescue alignments per read pair. The default value is 10.	--max-rescues	0–1023
min-score-coeff	Sets adjustment to aln-min-score per read base.	--Aligner.min-score-coeff	-64–63.999
mismatch-pen	Defines the score penalty for a mismatch.	--Aligner.mismatch-pen	0–63
no-unclip-score	When set to 1, the option removes any unclipped bonus (unclip-score) contributing to an alignment from the alignment score before further processing.	--Aligner.no-unclip-score	0–1
no-unpaired	Determines if only properly paired alignments should be reported for paired reads.	--Aligner. no-unpaired	0–1
pe-max-penalty	Specifies the maximum pairing score penalty for unpaired or distant ends.	--Aligner.pe-max-penalty	0–255
pe-orientation	Specifies the expected paired-end orientation. The following values represent the different orientations: 0 is FR (default) 1 is RF 2 is FF	--Aligner.pe-orientation	0–2
rescue-sigmas	Sets deviations from the mean read length used for rescue scan radius. The default value is 2.5.	--Aligner.rescue-sigmas
sec-aligns	Restricts the maximum number of secondary (suboptimal) alignments to report per read.	--Aligner.sec-aligns	0–4095
sec-aligns-hard	If set to 1, forces the read to be unmapped when not all secondary alignments can be output.	--Aligner.sec-aligns-hard	0–1
sec-phred-delta	Controls which secondary alignments are emitted. Only secondary alignments within this Phred value of the primary are reported.	--Aligner.sec-phred-delta	0–255
sec-score-delta	Determines the pair score threshold below primary that secondary alignments are allowed.	--Aligner. sec-score-delta
supp-aligns	Restricts the maximum number of supplementary (chimeric) alignments to report per read.	--Aligner.supp-aligns	0–4095
supp-as-sec	Determines if supplementary alignments should be reported with secondary flag.	--Aligner.supp-as-sec	0–1
supp-min-score-adj	Specifies amount to increase minimum alignment score for supplementary alignments. The score is computed by host software as 8 * match-score for DNA. The default is 0 for RNA.	--Aligner. supp-min-score-adj
unclip-score	Specifies the score bonus for reaching the edge of the read.	--Aligner.unclip-score	0–127
unpaired-pen	Specifies the penalty for unpaired alignments, using Phred scale.	--Aligner.unpaired-pen	0–255

If you disable automatic detection of insert-length statistics via the --enable-sampling option, you must override all the following options to specify the statistics. For more information, see [Mean Insert Size Detection]{.underline}. These options are part of the [Aligner] section of the configuration file.

Option	Description	Command Line Equivalent	Value
pe-stat-mean-insert	Specifies the average template length.	--pe-stat-mean-insert	0–65535
pe-stat-mean-read-len	Specifies the average read length.	--pe-stat-mean-read-len	0–65535
pe-stat-quartiles-insert	Specifies a comma-delimited trio of numbers for the 25th, 50th, and 75th percentile template lengths.	--pe-stat-quartiles-insert	0–65535
pe-stat-stddev-insert	Specifies the standard deviation of template length distribution.	--pe-stat-stddev-insert	0–65535

Variant Caller Options

The following options are in the Variant Caller section of the configuration file. For more information on these options, see [Variant Caller Options]{.underline}.

Name	Description	Command Line Equivalent	Value
dn-cnv-vcf	For de novo calling, filters joint structural variant VCF from the CNV calling step. If omitted, DRAGEN skips any checks with overlapping copy number variants.	--dn-cnv-vcf
dn-input-vcf	For de novo calling, filters joint small variant VCF from the de novo calling step.	--dn-input-vcf
dn-output-vcf	For de novo calling, specifies the file location for writing the filtered VCF file. If not specified, the input VCF is overwritten.	--dn-output-vcf
dn-sv-vcf	For de novo calling, filters the joint structural variant VCF file from the SV calling step. If omitted, DRAGEN skips any checks with overlapping structural variants.	--dn-sv-vcf
enable-joint-genotyping	To enable the joint genotyping caller, set to true.	--enable-joint-genotyping	true/false
enable-multi-sample-gvcf	Enables generation of a multisample gVCF file. If set to true, requires a combined gVCF file as input.	--enable-multi-sample-gvcf	true/false
enable-vlrd	Enables Virtual Long Read Detection.	--enable-vlrd	true/false
pedigree-file	Specifies the path to a pedigree file that describes the familial relationships between panels (specific to joint calling). Only pedigree files that contain trios are supported.	--pedigree-file
qc-snp-DeNovo-quality-threshold	Sets the threshold for counting and reporting de novo SNP variants.	--qc-snp-DeNovo-quality-threshold
qc-indel-DeNovo-quality-threshold	Sets the threshold for counting and reporting de novo INDEL variants.	--qc-indel-DeNovo-quality-threshold
variant	Specifies the path to a single gVCF file. You can use the --variant option multiple times to specify paths to multiple gVCF files. Use one file per line. Up to 500 gVCFs are supported.	--variant
variant-list	Specifies the path to a file containing a list of input gVCF files that need to be combined. Use one file per line.	--variant-list
vc-af-call-threshold	If the AF filter is enabled using --vc-enable-af-filter=true, the option sets the allele frequency call threshold for nuclear chromosomes to emit a call in the VCF. The default value is 0.01.	--vc-af-call-threshold
vc-af-filter-threshold	If the AF filter is enabled using --vc-enable-af-filter=true, the option sets the allele frequency filter threshold for nuclear chromosomes to mark emitted VCF calls as filtered. The default value is 0.05.	--vc-af-filter-threshold
vc-af-call-threshold-mito	If the AF filter is enabled using --vc-enable-af-filter-mito=true, the option sets the allele frequency call threshold to emit a call in the VCF for mitochondrial variant calling. The default value is 0.01.	--vc-af-call-threshold-mito
vc-af-filter-threshold-mito	If the AF filter is enabled using --vc-enable-af-filter-mito=true, the option sets the allele frequency filter threshold to mark emitted VCF calls as filtered for mitochondrial variant calling. The default value is 0.02.	--vc-af-filter-threshold-mito
vc-callability-normal-threshold	Specifies the normal sample coverage threshold for a site to be considered callable in the somatic callable regions report. The default is 5.	--vc-callability-normal-thresh
vc-callability-tumor-threshold	Specifies the tumor sample coverage threshold for a site to be considered callable in the somatic callable regions report. The default is 50.	--vc-callability-tumor-thresh
vc-clustered-event-penalty	SQ score penalty applied to phased clustered somatic events; set to 0 to disable the penalty. The default value is 4.0 for tumor-normal and 7.0 for tumor-only.	--vc-clustered-event-penalty
vc-decoy-contigs	Specifies the path to a comma-separated list of contigs to skip during variant calling.	--vc-decoy-contigs
vc-depth-annotation-threshold	Filters all non-PASS somatic alt variants with a depth below this threshold. The default value is 0 (no filtering).	--vc-depth-annotation-threshold
vc-depth-filter-threshold	Filters all somatic variants (alt or homref) with a depth below this threshold. The default value is 0 (no filtering).	--vc-depth-filter-threshold
vc-emit-ref-confidence	Enables base pair resolution gVCF generation or banded gVCF generation.	--vc-emit-ref-confidence	BP_RESOLUTION GVCF
vc-enable-af-filter	Enables the allele frequency filter of nuclear chromosomes for somatic mode. The default value is false.	--vc-enable-af-filter	true/false
vc-enable-af-filter-mito	Enables the allele frequency filter for mitochondrial variant calling. The default value is true.	--vc-enable-af-filter-mito	true/false
vc-enable-baf	Enables B-allele frequency output. The default value is true.	--vc-enable-baf	true/false
vc-enable-decoy-contigs	Enables variant calls on decoy contigs. The default value is false.	--vc-enable-decoy-contigs	true/false
vc-enable-liquid-tumor-mode	Enables liquid tumor mode for tumor-normal analysis to account for tumor-in-normal contamination. The default value is false.	--vc-enable-liquid-tumor-mode	true false
vc-enable-non-homref-normal-filter	Enables the nonhomref normal filter, which filters out somatic variants if the normal sample genotype is not homozygous reference. The default value is true.	--vc-enable-non-homref-normal-filter	true/false
vc-enable-orientation-bias-filter	Enables the orientation bias filter. The default value is false, which means the option is disabled.	--vc-enable-orientation-bias-filter	true/false
vc-enable-phasing	Enables variants to be phased when possible. The default value is true.	--vc-enable-phasing	true/false
vc-combine-phased-variants-distance	When the specified value is greater than 0, combines all phased variants in the phasing set that have a distance less than or equal to the provided value. The max allowed phasing distance is 15. The default value is 0, which disables the option.	--vc-combine-phased-variants-distance	0–15
vc-enable-roh	Enables the ROH caller and output. The default value is true.	--vc-enable-roh	true/false
vc-enable-triallelic-filter	Enables the multiallelic filter for somatic mode. The default value is false.	--vc-enable-triallelic-filter	true/false
vc-enable-non-primary-allelic-filter	Similar to vc-enable-triallelic-filter, but less aggressive. Keep the allele per position with highest alt AD, and only filter the rest. The default is false. Not compatible with vc-enable-triallelic-filter.	--vc-enable-non-primary-allelic-filter	true/false
vc-enable-vcf-output	Enables VCF file output during a gVCF run. The default value is false.	--vc-enable-vcf-output	true/false
vc-enable-unequal-ntd-errors	Enables the Sample-specific SNV Error Estimation feature. The default value is true for somatic pipelines and false for germline pipelines.	--vc-enable-unequal-ntd-errors	true/false/auto
vc-enable-trimer-context	When enabled along with vc-enable-unequal-ntd-errors, DRAGEN uses trimer rather than monomer context to estimate SNV error rates. The default value is false, except when vc-enable-umi-liquid is enabled.	--vc-enable-trimer-context	true/false
vc-ntd-error-params	Params file for per-nucleotide error rate calibration.	--vc-ntd-error-params	*.snperror-sampler.log
vc-estimate-ntd-error	Override whether to run ntd error rate estimation	--vc-estimate-ntd-error	true/false
vc-forcegt-vcf	Forces genotyping for small variant calling. A file (*.vcf or *.vcf.gz) containing a list of small variants is required.	--vc-forcegt-vcf	*.vcf or *.vcf.gz file specifying the small variants to force genotype.
vc-gvcf-bands	Define bands for gVCF output. The default value is 1 10 20 30 40 60 80 for germline calling and 1 3 10 20 50 80 for somatic. If enable-multi-sample-gvcf is enabled, the default value is 5, 20, 60.	--vc-gvcf-bands
vc-gvcf-homref-lod	Sets the limit of detection for somatic homref calls. The default value is 0.05.	--vc-gvcf-homref-lod
vc-hard-filter	Uses a list of Boolean expressions to filter variant calls. The default expression is HardQUAL:all: QUAL < 10.4139;LowDepth:all: DP < 1	--vc-hard-filter	QD MQ FS MQRankSum ReadPosRankSum QUAL DP GQ
vc-homref-depth-filter-threshold	In gvcf mode, filters all somatic homref variants with a depth below this threshold. The default value is 3.	--vc-homref-depth-filter-threshold
vc-max-alternate-alleles	Specifies the maximum number of ALT alleles to output in a VCF or gVCF. The default value is 1000.	--vc-max-alternate-alleles
vc-max-reads-per-active-region	Specifies the maximum number of reads for an active region for downsampling. The default value is 10000.	--vc-max-reads-per-active-region
vc-max-reads-per-active-region-mito	Specifies the maximum number of reads for an active region of mitochondrial small variant calling. The default value is 40000.	--vc-max-reads-per-active-region-mito
vc-max-reads-per-raw-region	Specifies the maximum number of reads per raw region for downsampling. The default value is 30000.	--vc-max-reads-per-raw-region
vc-max-reads-per-raw-region-mito	Specifies the maximum number of reads covering a specified raw region of mitochondrial small variant calling. The default value is 40000.	--vc-max-reads-per-raw-region-mito
vc-min-base-qual	Specifies the minimum base quality to be considered in the active region detection of the small variant caller. The default value is 10.	--vc-min-base-qual
assembler-min-contig-qual	Specifies the minimum base quality to be considered for De Bruijn graph construction. The default value is 10.	--assembler-min-contig-qual
vc-min-tail-qual	Specifies the minimum base quality to trim consecutive bases on either end of a read. The default value is 10.	--vc-min-tail-qual
vc-min-call-qual	Specifies the minimum variant call quality for emitting a call. The default value is 3.	--vc-min-call-qual
vc-min-read-qual	Specifies the minimum read quality (MAPQ) to be considered for small variant calling. The following default values exist: 1 for germline 3 for somatic T/N 20 for somatic T-only	--vc-min-read-qual
vc-min-reads-per-start-pos	Specifies the minimum number of reads per start position for downsampling. The default value is 10.	--vc-min-reads-per-start-pos
vc-min-tumor-read-qual	Specifies the minimum tumor read quality (MAPQ) to be considered for variant calling.	--vc-min-tumor-read-qual
vc-orientation-bias-filter-artifacts	Specifies the artifact type to be filtered. An artifact, or an artifact and the reverse compliment of the artifact, cannot be listed twice.	--vc-orientation-bias-filter-artifacts	C/T, G/T C/T, G/T, C/A
vc-output-variant-read-position	Enables outputting the variant read position in the INFO field. The default value is false.	--vc-output-variant-read-position	true/false
vc-override-tumor-pcr-params-with-normal	Ignores the tumor sample parameters and uses the normal sample parameters for analysis of both samples. The default value is true.	--vc-override-tumor-pcr-params-with-normal	true/false
vc-remove-all-soft-clips	If set to true, the variant caller does not use soft clips of reads to determine variants. The default value is false.	--vc-remove-all-soft-clips	true/false
vc-roh-blacklist-bed	If provided, the ROH caller ignores variants that are contained in any region in the block list BED.	--vc-roh-blacklist-bed
vc-sq-call-threshold	Sets the SQ call threshold to emit a call in the VCF. The default value is 3.0 for tumor-normal and 0.1 for tumor-only.	--vc-sq-call-threshold
vc-sq-filter-threshold	Sets the SQ filter threshold mark calls as filtered in the VCF. The default value is 17.5 for tumor-normal and 3.0 for tumor-only.	--vc-sq-filter-threshold
vc-somatic-hotspots	Provides a file to override the default hotspots file.	--vc-somatic-hotspots
vc-use-somatic-hotspots	If set to false, disables the use of somtic hotspots.	--vc-use-somatic-hotspots	true/false
vc-hotspot-log10-prior-boost	Specifies the magnitude by which the prior probabilities of hotspot variants are boosted (default: 4.0).	--vc-hotspot-log10-prior-boost
vc-target-bed	Restricts processing of the small variant caller, target BED related coverage, and callability metrics to regions specified in a BED file.	--vc-target-bed	*.bed file
vc-target-bed-padding	Specifies a number of bases that the small variant caller then uses to pad each target BED region. The default value is 0. .	--vc-target-bed-padding
vc-target-coverage	Specifies the target coverage for downsampling. The default value is 500 for germline and 50 for somatic mode.	--vc-target-coverage
vc-target-coverage-mito	Specifies the maximum number of reads with a start position overlapping any given position for mitochondrial small variant calling. The default value is 40000.	--vc-target-coverage-mito
vc-target-vaf	Specifies an allele frequency above which haplotypes will be considered by the caller as potentially appearing in the sample. Default=0.03.	--vc-target-vaf	[0, 1]
vc-tin-contam-tolerance	Sets the maximum tumor-in-normal contamination expected. Setting this to a nonzero value enables liquid tumor mode. If liquid tumor mode is enabled, the default value is 0.15. If liquid tumor mode is disabled, the default value is 0.	--vc-tin-contam-tolerance
vc-excluded-regions-bed	Somatic mode only: if provided, variants that overlap with the regions in the BED file are hard-filtered and marked as "excluded_regions" in the filter column.	--vc-excluded-regions-bed	*.bed file
vc-systematic-noise	Specifies a BED file with site-specific systematic noise level to calculate AQ score (systematic noise score).	--vc-systematic-noise
vc-systematic-noise-filter-threshold	Sets the AQ threshold for applying the systematic-noise filter. The default value is 10 for tumor-normal and 60 for tumor-only.	--vc-systematic-noise-filter-threshold	0–100
vc-systematic-noise-filter-threshold-in-hotspot	Sets the AQ threshold for applying the systematic-noise filter to hotspot variants. The default value is 10 for tumor-normal and 20 for tumor-only.	--vc-systematic-noise-filter-threshold-in-hotspot	0–100
vc-enable-germline-tagging	Enable germline variant tagging using population databases. The default is false. Once enabled, it will also require user to specify Nirvana parameters. Details can be found in somatic small variant calling section.	--vc-enable-germline-tagging	true/false
germline-tagging-db-threshold	The minimum alternative allele count in population database for a variant to be defined as germline. The default value is 50.	--germline-tagging-db-threshold
germline-tagging-pop-af-threshold	The minimum population allele frequency for a variant to be defined as germline. Once specified, this will ignore the input from --germline-tagging-db-threshold.	--germline-tagging-pop-af-threshold

Nirvana Annotation Options

Name	Description	Command Line Equivalent	Value
enable-variant-annotation	Enable Nirvana variant annotation on the output vcf/gvcf files. The default is false.	--enable-variant-annotation	true/false
variant-annotation-data	Top directory containing Nirvana data file. Dowloadable at https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/Nirvana_DownloadData_fDG.htm	--variant-annotation-data
variant-annotation-assembly	Genome assembly to use for variant annotation.	--variant-annotation-assembly	GRCh37/GRCh38

Mutation Annotation Format (MAF) Conversion Options

Name	Description	Command Line Equivalent	Value
enable-maf-output	Enables Mutation Annotation Format (MAF) output. The default value is false.	--enable-maf-output	true/false
maf-transcript-source	Specifies desired transcript source for Mutation Annotation Format (MAF) output.	--maf-transcript-source	Refseq/Ensembl
maf-input-vcf	Specifies input VCF file for standalone Mutation Annotation Format (MAF) output.	--maf-input-vcf	*.hard-filtered.vcf.gz file
maf-input-json	Specifies input JSON file for standalone Mutation Annotation Format (MAF) output.	--maf-input-json	*.hard-filtered.vcf.annotated.json.gz file
maf-include-non-pass-variants	Enables all variants, including non-PASS variants, output. THe default value is false.	--maf-include-non-pass-variants	true/false

CNV Caller Options

The following options are applicable to the CNV caller.

Name	Description	Command Line Equivalent	Value
cnv-bypass-contig-check	Bypass contig check for self normalization.	--cnv-bypass-contig-check	true/false
cnv-cbs-alpha	Specifies the significance level for the test to accept change points. The default value is 0.01.	--cnv-cbs-alpha
cnv-cbs-eta	Specifies the type I error rate of the sequential boundary for early stopping when using the permutation method. The default value is 0.05.	--cnv-cbs-eta
cnv-cbs-kmax	Specifies the maximum width of smaller segment for permutation. The default value is 25.	--cnv-cbs-kmax
cnv-cbs-min-width	Specifies the minimum number of markers for a changed segment. The default value is 2.	--cnv-cbs-min-width	[2,5]
cnv-cbs-nmin	Specifies the minimum length of data for maximum statistic approximation. The default value is 200.	--cnv-cbs-nmin
cnv-cbs-nperm	Specifies the number of permutations used for p-value computation. The default value is 10000.	--cnv-cbs-nperm
cnv-cbs-trim	Specifies the proportion of data to be trimmed for variance calculations. The default value is 0.025.	--cnv-cbs-trim
cnv-counts-method	Specifies the overlap method for counting an alignment.	--cnv-counts-method	midpoint / start / overlap
cnv-enable-filter-copy-ratio	Enable cnvCopyRatio filtering based on fixed threshold values. Default true for germline analysis	--cnv-enable-filter-copy-ratio	true/false
cnv-enable-gcbias-correction	Enables GC bias correction. The default is true.	--cnv-enable-gcbias-correction	true/false
cnv-enable-gcbias-smoothing	Enables smoothing across GC bins. The default value is true. The default value is true.	--cnv-enable-gcbias-smoothing	true/false
cnv-enable-gender-matched-pon	Enable gender matched PON normalization. The default value is true.	--cnv-enable-gender-matched-pon	true/false
cnv-enable-ref-calls	When set to true, copy neutral (REF) calls are included in the output VCF.	--cnv-enable-ref-calls	true/false
cnv-enable-self-normalization	Enables self-normalization.	--cnv-enable-self-normalization	true/false
cnv-enable-tracks	Enables generation of track files that can be imported into IGV for viewing. The default is true.	--cnv-enable-tracks	true/false
cnv-exclude-bed	Specifies regions to blocklist for CNV processing.	--cnv-exclude-bed
cnv-exclude-bed-min-overlap	Specifies the minimum fraction of overlap between target intervals and the blocklist to exclude target from the list.	--cnv-exclude-bed-min-overlap	[0.0, 1.0]
cnv-extreme-percentile	Specifies the extreme median percentile value used to filter out samples. The default value is 2.5.	--cnv-extreme-percentile	[0.0, 100.0]
cnv-filter-bin-count	Minimum number of bins to pass a call (currently only applied to somatic WGS calls)	--cnv-filter-bin-count	[0.0, inf)
cnv-filter-bin-support-ratio	If the span of supporting bins is less than the specified ratio with respect to the overall event length, the option filters out a candidate event. The default ratio is 0.2 (20% support).	--cnv-filter-bin-support-ratio	[0.0, 1.0]
cnv-filter-bin-support-ratio-min-len	Mininum event length to apply cnv-filter-bin-support-ratio (currently only applied for germline WGS calls). Default value of 80000.	--cnv-filter-bin-support-ratio-min-len	[0.0, inf]
cnv-filter-copy-ratio	Specifies the minimum copy ratio threshold value centered about 1.0 at which a reported event is marked as PASS in the output VCF file. The default value is 0.2.	--cnv-filter-copy-ratio	[0.0, 1.0]
cnv-filter-del-mean	SM value used to hard filter DELs in CNV VCF (Somatic WGS) when the caller returns the default model (purity: NA). Default is automatically computed based on the variance of the sample.	--cnv-filter-del-mean	[0.0, 1.0]
cnv-filter-dup-mean	SM value used to hard filter DUPs in CNV VCF (Somatic WGS) when the caller returns the default model (purity: NA). Default is automatically computed based on the variance of the sample.	--cnv-filter-dup-mean	[1.0, inf)
cnv-filter-de-novo-quality	Sets the Phred-scale threshold for calling an event as de novo in the proband.	--cnv-filter-de-novo-quality	[0, inf)
cnv-filter-duplicate-alignments	Filter duplicate marked alignments during target counts if option is set to true. Require enable-duplicate-marking=true	--cnv-filter-duplicate-alignments	true/false
cnv-filter-length	Specifies the minimum event length in bases at which a reported event is marked as PASS in the output VCF file. The default value is 10000.	--cnv-filter-length	[0, inf)
cnv-filter-limit-of-detection	Target limit of detection for enrichment somatic CNV alternative hypothesis test. The default value is 0.2.	--cnv-filter-limit-of-detection	[0.0, inf)
cnv-filter-qual	Specifies the QUAL value at which a reported event is marked as PASS in the output VCF file.	--cnv-filter-qual	[0, inf)
cnv-generate-pon-metric-file	Generate PON metric file for WES/targeted panel.	--cnv-generate-pon-metric-file	true/false
cnv-input	Specifies a CNV input file instead of a BAM. Files can be target.counts.gz or tn.tsv.gz for de novo.	--cnv-input
cnv-interval-width	Specifies the width of the sampling interval for CNV WGS processing.	--cnv-interval-width	[100, inf)
cnv-max-percent-zero-samples	Specifies the number of zero coverage samples allowed for the target. If the target exceeds the specified threshold, then the target is filtered out. The default value is 5%.	--cnv-max-percent-zero-samples	[0.0, 100.0]
cnv-max-percent-zero-targets	Specifies the number of zero coverage targets allowed for the sample. If the sample exceeds the specified threshold, then the sample is filtered out. The default value is 5%.	--cnv-max-percent-zero-targets	[0.0, 100.0]
cnv-merge-distance	Specifies the maximum segment gap allowed for merging segments. The default value for Somatic WGS is 10k, for Germline WGS is 0. Default is inf when using CNV WES workflows.	--cnv-merge-distance	[0, inf)
cnv-merge-threshold	Specifies the maximum segment mean difference to merge two adjacent segments. The segment mean is represented as a linear copy ratio value.	--cnv-merge-threshold	[0.0, inf)
cnv-min-mapq	Specifies the minimum MAPQ for alignment to be counted.	--cnv-min-mapq	[1, inf)
cnv-normal-b-allele-vcf	Normal sample SNV VCF for determining het sites.	--cnv-normal-b-allele-vcf
cnv-normal-cnv-vcf	Matched-normal CNV calls.	--cnv-normal-cnv-vcf
cnv-normals-file	Specifies a single file to be used in the panel of normals. You can use the option multiple times, once for each file.	--cnv-normals-file
cnv-normals-list	Specifies a text file containing paths to the list of reference target counts files to use as a panel of normals.	--cnv-normals-list
cnv-num-gc-bins	Specifies the number of bins for GC bias correction. Each bin represents the GC content percentage. The default value is 25.	--cnv-num-gc-bins	10 20 25 50 100
cnv-num-singular-values	Number of singular values to retain for tangent normalization. The default is 5 when cnv-segmentation-mode=bed, otherwise dynamically detected.	--cnv-num-singular-values	[1, inf)
cnv-ploidy	Specifies the normal ploidy value. Used for estimating the copy number value emitted in the output VCF file. The default value is 2.	--cnv-ploidy
cnv-population-b-allele-vcf	CNV population SNP input VCF file.	--cnv-population-b-allele-vcf
cnv-qual-length-scale	Specifies the bias weighting factor to adjust QUAL estimates for segments with longer lengths. The default value is 0.9303 (2-0.1) and should not need to be modified.	--cnv-qual-length-scale	[0.0, 1.0]
cnv-qual-noise-scale	Specifies the bias weighting factor to adjust QUAL estimates based on sample variance. The default value is 1.0 and should not need to be modified.	--cnv-qual-noise-scale	[1.0, 10.0]
cnv-segmentation-mode	Specifies the segmentation algorithm to perform.	--cnv-segmentation-mode	cbs slm hslm aslm
cnv-somatic-enable-lower-ploidy-limit	Enable check on lower ploidy limit based on essential genes. Default true.	--cnv-somatic-enable-lower-ploidy-limit	true/false
cnv-somatic-essential-genes-bed	BED file containing genes (regions) where the model should not predict HOMDELs. A default set of regions will be used if this is not provided.	--cnv-somatic-essential-genes-bed
cnv-skip-contig-list	A comma-separated list of contig identifiers to skip when generating intervals for WGS analysis. If not specified, the following contigs are skipped by default: chrM,MT,m,chrm.	--cnv-wgs-skip-contig-list
cnv-slm-eta	Sets the baseline probability that the mean process changes its value. A higher value increases SLM segmentation sensitivity. The default value is 4e–5.	--cnv-slm-eta	[0, inf)
cnv-slm-fw	Specifies the minimum number of data points for a CNV to be emitted. The default value is 0.	--cnv-slm-fw
cnv-slm-omega	Sets the scaling parameter modulating relative weight between experimental/biological variance. The default value is 0.3.	--cnv-slm-omega	[0, inf)
cnv-slm-stepeta	Specifies the distance normalization parameter. The default value is 10000. Only valid for HSLM.	--cnv-slm-stepeta	[0, inf)
cnv-target-bed	Specifies a properly formatted BED file that indicates the target intervals to use for sample coverage. Use in WES analysis.	--cnv-target-bed
cnv-target-factor-threshold	Specifies the bottom percentile of panel-of-normals medians to filter out useable targets. The default value is 1% for whole genome processing and 5% for targeted sequencing processing.	--cnv-target-factor-threshold
cnv-truncate-threshold	Sets the percent threshold used to truncate extreme outliers. The default value is 0.1%.	--cnv-truncate-threshold
cnv-use-somatic-vc-baf	Use somatic SNV BAFs from VC for B allele counting.	--cnv-use-somatic-vc-baf
cnv-use-somatic-vc-vaf	Use somatic SNV VAFs from VC to help determine purity and ploidy.	--cnv-use-somatic-vc-vaf

Structural Variant Caller Options

Name	Description	Command Line Equivalent	Range
enable-sv	Enables the structural variant caller. The default value is false.	--enable-sv	true/false
sv-call-regions-bed	Specifies a BED file containing the set of regions to call. Optionally, you can compress the file in GZIP or BZIP format.	--sv-call-regions-bed
sv-denovo-scoring	Enables de novo quality scoring for structural variant joint diploid calling. Provide the pedigree file as well.	--sv-denovo-scoring
sv-forcegt-vcf	Specifies a VCF of structural variants for forced genotyping. The variants are scored and included in the output VCF, even if not found in the sample data. The variants are merged with any additional variants discovered directly from the sample data.	--sv-forcegt-vcf
sv-discovery	Enables SV discovery. Set to false when using --sv-forcegt-vcf to indicate that SV discovery should be disabled and only the forced genotyping input should be used.	--sv-discovery	true/false
sv-exome	When set to true, configures the variant caller for targeted sequencing inputs, which includes disabling high depth filters. The default value is false unless --enable-map-align=true and there is not more than 50 Gb of sequencing input.	--sv-exome	true/false
sv-output-contigs	Set to true to have assembled contig sequences output in a VCF file. The default value is false.	--sv-output-contigs	true/false
sv-region	Limits the analysis to a specified region of the genome for debugging purposes. You can use the option multiple times to build a list of regions.	--sv-region	Must be in the format chr:startPos-endPos.

VNTR Caller Options

The following options pertain to the VNTR Caller. For more information on these options, see the VNTR Calling page.

Name	Description	Command Line Equivalent	Range
enable-vntr	Enables the VNTR caller (default value is false).	--enable-vntr	true/false
vntr-num-threads	Sets the number of threads used by the VNTR caller (default value is 36).	--vntr-num-threads	integer: [1, max available]
vntr-catalog-bed	Specifies the set of regions considered by the VNTR caller, formatted as a BED file. Optionally the bed file can be compressed in GZIP format.	--vntr-catalog-bed
vntr-normalization-regions-bed	Specifies a BED file of regions free of large variants to be used as a baseline for custom references.	--vntr-normalization-regions-bed
vntr-priors-model	Specifies the priors model to be used by the VNTR genotyper: 1 is no priors, 2 is a set of 4 priors based on genotype, 3 is population allele-based priors. Default is 3 with a default set of population priors. If 3 is used with a custom reference then a vntr-priors-file must also be provided.	--vntr-priors-model	1, 2, or 3
vntr-priors-file	Specifies a set of population allele priors to be used for the VNTR genotyper as a JSON file. Required for a custom reference with the vntr-priors-model set to 3.	--vntr-priors-file
sv-vntr-merge	Integrates the VNTR calls into the SV output VCF when both VNTR and SV calling are enabled (default value is true). Also splits multi-allelic VNTR calls, filters short VNTR calls, and filters overlapping SV calls in the SV VCF.	--sv-vntr-merge	true/false
sv-vntr-filter-total-calls	Applies "TotalCall" filter to VNTR "total calls" with GT=./. reported in merged SV VCF when both VNTR and SV calling are enabled (default value is true).	--sv-vntr-filter-total-calls	true/false

Repeat Expansion Detection Options

The following options can be set in the RepeatGenotyping section of the configuration file or on the command line. For more information, see Repeat Expansion Detection with Expansion Hunter [on page 1]{.underline}.

Name	Description	Command Line Equivalent	Range
enable	Enables repeat expansion detection.	--repeat-genotype-enable	true/false
specs	Specifies the full path to the JSON file that contains the repeat variant catalog (specification) describing the loci to call.	--repeat-genotype-specs
use-catalog	Repeat variant catalog type to use (default - ~60 repeats, default_plus_smn - same as default with SMN repeat, expanded - ~50K repeats).	--repeat-genotype-use-catalog	default/default_plus_smn/expanded

Repeat Profiling Options

Name	Description	Command Line Equivalent	Range
enable-str-profiler	Enables the STR profiler module	--enable-str-profiler	true/false
str-profiler-sample-name	A name to identify the sample in downstream analyses (default: same as RGSM)	--str-profiler-sample-name
str-profiler-output-directory	Specify a directory where to save the STR profile into (default: same as --ouput-directory)	--str-profiler-output-directory
str-profiler-analysis	Specify an analysis to be performed on the samples cohort	--str-profiler-analysis	outlier/casecontrol
str-profiler-controls-directory	Specify the directory containing the profiles for the control samples (required by --str-profiler-analysis)	--str-profiler-controls-directory
str-profiler-cases-directory	Specify the directory containing the profiles for the cases samples (required by --str-profiler-analysis)	--str-profiler-cases-directory
str-profiler-regions-bed	Specify the path to a file in BED format containing regions to restrict the analysis to	--str-profiler-regions-bed
str-profiler-resampling-rounds	Specify how many times to resample the read counts during outlier analysis (default: 1000)	--str-profiler-resampling-rounds	Integer [3-Inf)
str-profiler-threads	Specify how many threads to use during resampling (default: 48)	--str-profiler-threads	Integer [1-Inf)
str-profiler-min-anchored-mapq	Minimum mapping quality for a read to be considered an anchor (default: 50)	--str-profiler-min-anchored-mapq	Integer [0-Inf)
str-profiler-max-irr-mapq	Maximum mapping quality for a read entropy to be computed (default: 40)	--str-profiler-max-irr-mapq	Integer [0-Inf)
str-profiler-shortest-unit-to-consider	Shortest motif size to evaluate (default: 2)	--str-profiler-shortest-unit-to-consider	Integer [2-Inf)
str-profiler-longest-unit-to-consider	Longest motif size to evaluate (default: 20)	--str-profiler-longest-unit-to-consider	Integer [2-Inf)

RNA-seq Options

Name	Description	Command Line Equivalent	Range
enable-rna	Enables processing of RNA-seq data.	--enable-rna	true/false
annotation-file	Use to supply a gene annotation file. Required for quantification and gene-fusion.	--annotation-file, -a	Path to GTF/GFF file
enable-rna-quantification	Enables RNA quantification.	--enable-rna-quantification	true/false
enable-rna-gene-fusion	Enables RNA gene fusion calling.	--enable-rna-gene-fusion	true/false

UMI Options

Name	Description	Command Line Equivalent	Range
umi-library-type	Sets the batch option for correcting UMIs. Not required.	--umi-library-type	random-duplex random-simplex nonrandom-duplex
umi-enable	Enables UMI-based read processing.	--umi-enable	true/false
vc-enable-umi-solid	Enables solid tumor UMI-aware VC settings. The default value is false.	--vc-enable-umi-solid	true/false
vc-enable-umi-liquid	Enables liquid tumor UMI-aware VC settings. The default value is false.	--vc-enable-umi-liquid	true/false
vc-enable-umi-germline	Allow germline VC from UMI-collapsed reads. The default value is false.	--vc-enable-umi-germline	true/false
umi-correction-scheme	Describes the methodology to use for correcting sequencing errors in UMIs.	--umi-correction-scheme	lookup random none positional
umi-correction-table	Provides the path to the correction table for lookup correction scheme. .	--umi-correction-table	Path to table file
umi-emit-multiplicity	Sets the consensus read output type.	--umi-emit-multiplicity	both duplex simplex
umi-min-supporting-reads	Specifies the number of input reads with matching UMI and position required to generate a consensus read.	--umi-min-supporting-reads	Integer ≥ 1. The default is 2.
umi-metrics-interval-file	Provides the path to target regions file used for UMI on target metrics.	--umi-metrics-interval-file	Path to valid BED file
umi-source	Specifies the location to read UMIs from.	--umi-source	qname bamtag fastq
umi-fastq	Provides the path to a separate FASTQ file with UMI sequences for each read.	--umi-fastq	Path to valid FASTQ file
umi-nonrandom-whitelist	Provides the path to a file containing valid nonrandom UMIs sequences. Enter one path per line.	--umi-nonrandom-whitelist
umi-fuzzy-window-size	Collapses reads with matching UMIs and alignment positions up to the distance specified.	--umi-fuzzy-window-size	Integer ≥ 1. The default is 3.
umi-output-uncollapsed-bam	Enable raw reads BAM output	--umi-output-uncollapsed-bam	true/false

Systematic Noise BED Creation Options

The following options are applicable to create the systematic noise BED file from normal VCFs.

Step 1. Run DRAGEN somatic tumor-only pipeline on each of approximately 50 normal samples.

Name	Description	Command Line Equivalent	Value
vc-detect-systematic-noise	Runs the tumor-only pipeline in a very sensitive mode that aims to capture noise. Use --tumor-fastq1/2 or --tumor-bam-input to specify input reads. This step requires vc-enable-germline-tagging=true. To explicitly run without germline tagging, use vc-skip-germline-tagging=true. VCFs generated with this setting can be used in step 2 when building a systematic noise file from normal samples. This mode is not intended for analyzing tumor samples. The default value is false.	--vc-detect-systematic-noise	true/false
vc-enable-germline-tagging	Enable germline variant tagging using population databases. The default is false. Once enabled, it will also require user to specify Nirvana parameters. Details can be found in somatic small variant calling section. When used with noise generation it helps prevent treating germline sites as noisy. It is strongly recommended to enable this option when generating VCFs for the normal samples.	--vc-enable-germline-tagging	true/false

Step 2. Generate the final noise file with:

Name	Description	Command Line Equivalent	Value
build-sys-noise-vcfs-list	Path to text file containing list of normal VCF/GVCF files (from step 1) to be included in the systematic noise. One file per line.	--build-sys-noise-vcfs-list
build-sys-noise-germline-vaf-threshold	Minimum variant allele frequency threshold to define germline variants. Variants with AF higher than this threshold will not contribute to the noise file. Set to 1 to disable.	--build-sys-noise-germline-vaf-threshold	Default=1. The valid range is [0-1].
build-sys-noise-use-germline-tag	If available in the VCF use germline tags to prevent germline calls from contributing to systematic noise.	--build-sys-noise-use-germline-tag	Default=true
build-sys-noise-threads	Max number of threads used during noise generation. Each thread consumes approx. 70 GB of system memory.	--build-sys-noise-threads	Options are 1 or 2. Default=2.
build-sys-noise-method	Method to compute noise across samples ['mean'/'max']. For higher specificity 'max' is recommended, for higher sensitivity 'mean' is recommended.	--build-sys-noise-method	Default=mean
build-sys-noise-decimal-precision	Number of decimal digits in noise file. Options are [3-6]. For typical WES/WGS with 50-500X coverage 3 decimal places should be sufficient. For deep UMI samples with low noise rates 5 decimal places are recommended. Lower precision may help reduce noise file size especially on WES/WGS. The default is set for accuracy.	--build-sys-noise-decimal-precision	Default=5
build-sys-noise-min-sample-cov	Min coverage at a site for a sample to be used towards noise estimation. At low coverages estimated allele frequencies become less reliable, but low coverage sites also tend to be noisy and useful for inclusion in the noise file.	--build-sys-noise-min-sample-cov	Default=5
build-sys-noise-min-supporting-samples	Min number of samples with noise at a position in order for a position to be considered systematic-noise	--build-sys-noise-min-supporing-samples	Default=2

Explify Options

There are three separate Explify capabilities available: the Explify analysis pipleine ("explify" prefix), a generalized metagenomics kmer classifier ("kmer-classifier" prefix), and a tool to build databases to be used by the kmer classifier ("kmer-class-db-builder" prefix).

Explify Analysis Pipeline Options

Name	Description	Command Line Equivalent	Range
enable-explify	Enables the Explify Pipeline. The default value is false	--enable-explify	true/false
explify-sample-list	Input sample list .tsv file with sample IDs, FASTQs, etc.	--explify-sample-list	See User Guide
explify-test-panel-name	Set test panel name	--explify-test-panel-name	"RPIP", "UPIP", "VSPv2", "Custom"
explify-test-panel-version	Set to test panel version (e.g. "7.3.2")	--explify-test-panel-version	See User Guide
explify-ref-db-dir	Path to root directory for Explify Database files	--explify-ref-db-dir
explify-load-db-ram	Option to load database into RAM if not on ramdisk. The default value is false.	--explify-load-db-ram	true/false
explify-no-read-qc	Option to turn off read QC on FASTQs before analysis. The default value is false.	--explify-no-read-qc	true/false
explify-internal-control	Option to set internal control from an accepted list. The default value is "Enterobacteria phage T7"	--explify-internal-control	See User Guide
explify-internal-control-concentration	Option to set internal control concentration in copies/mL of sample. The default value is 12100000.	--explify-internal-control-concentration	Integer > 0
explify-sensitivity-threshold	Option to set sensitivity threshold. The default value is 5.	--explify-sensitivity-threshold	0 < Integer < 1000. Only valid for VSPv2
explify-custom-ref-fasta	Reference Fasta file	--explify-custom-ref-fasta	Required for custom ref DBs
explify-custom-ref-bed	Reference BED file	--explify-custom-ref-bed	Optional for custom ref DBs
explify-ncpus	Option to set the number of CPUs available for processing	--explify-ncpus	[1,max avail]

Metagenomics Kmer Classifier Options

Name	Description	Command Line Equivalent	Range
enable-kmer-classifier	Enables the Kmer Classifier. The default value is false	--enable-kmer-classifier	true/false
kmer-classifier-input-read-file	Input sequence file (zipped or unzipped) to the Kmer Classifier	--kmer-classifier-input-read-file
kmer-classifier-db-file	Database of sequences to classify against	--kmer-classifier-db-file
kmer-classifier-load-db-ram	Load the database onto RAM. Do not use if database in on ramdisk. The default value is false	--kmer-classifier-load-db-ram	true/false
kmer-classifier-multiple-inputs	Set to true to run with multiple inputs. The input read file is now a .tsv file that has three columns: Sample ID, Read1 file, (optional) Read 2 file. The default value is false.	--kmer-classifier-multiple-inputs	true/false
kmer-classifier-min-window	The minimum number of consecutive kmers for classify assignment at taxid. The default value is 1	--kmer-classifier-min-window	Integer >=1
kmer-classifier-output-read-seq	Option to enable read sequence column in the output file. The default value is false	--kmer-classifier-output-read-seq	true/false
kmer-classifier-output-taxid-seq	Option to enable a taxid string column in the output file. The default value is false	--kmer-classifier-output-taxid-seq	true/false
kmer-classifier-db-to-taxid-json	Path to JSON file that maps database IDs to external taxids, names, and ranks	--kmer-classifier-db-to-taxid-json	See User Guide
kmer-classifier-no-read-output	Option to not create individual read output. The default value is false	--kmer-classifier-no-read-output	true/false
kmer-classifier-no-taxid-counts	Option to not write taxid count output file. The default value is false	--kmer-classifier-no-taxid-counts	true/false
kmer-classifier-protein-input	Option to indicate protein query sequences and database. The default value is false	--kmer-classifier-protein-input	true/false
kmer-classifier-remove-dups	Set to deduplicate reads in input files	--kmer-classifier-remove-dups	true/false
kmer-classifier-ncpus	Option to set the number of CPUs available for processing	--kmer-classifier-ncpus	[1,max avail]

Metagenomics Kmer Classifier Database Builder Options

Name	Description	Command Line Equivalent	Range
enable-kmer-class-db-builder	Enables the Kmer Classifier Database Builder. The default value is false	--enable-kmer-class-db-builder	true/false
kmer-class-db-builder-input-file	Headerless, tab-delimited file where each line is (1) path to a reference fasta file and (2) the associated taxid. When using --kmer-class-db-builder-taxids-as-seq-name, the second column is required but ignored	--kmer-class-db-builder-input-file
kmer-class-db-builder-kmer-length	Kmer length	--kmer-class-db-builder-kmer-length	[4, 64]
kmer-class-db-builder-gmer-length	Gmer length (must be >= kmer length)	--kmer-class-db-builder-gmer-length	[4, 64]
kmer-class-db-builder-tax-tree-file	.tri file with nodes in the taxonomic tree for a classifier database (not required if building binner database). Headerless, tab-delimited file where each line has (1) child node taxid and (2) parent node taxid.	--kmer-class-db-builder-tax-tree-file
kmer-class-db-builder-protein	Set to indicate input sequences are protein sequences. Default is false.	--kmer-class-db-builder-protein	true/false
kmer-class-db-builder-taxids-to-keep	File with taxids to keep. If set, any kmers with taxids not in this file will be excluded from database.	--kmer-class-db-builder-taxids-to-keep
kmer-class-db-builder-num-categories	Set to build binner database with this number of categories. Max is 25 categories, assumes categories are from 2^0..2^n sequentially. The categories take the place of taxids in the input file.	--kmer-class-db-builder-num-categories	Integer [0,25]
kmer-class-db-builder-save-weights	Set to build classification database that saves all kmers / taxids / weights.	--kmer-class-db-builder-save-weights	true/false
kmer-class-db-builder-kmer-cutoff	Cutoff that excludes k-mers that are found in more than cutoff number of taxids when building a database using --kmer-class-db-builder-save-weights. Helps speed up classification. (Default=1000)	--kmer-class-db-builder-kmer-cutoff	Integer
kmer-class-db-builder-mask-bits	Number of bits to mask in kmer before building / searching. (Deafult=7)	--kmer-class-db-builder-mask-bits	Integer
kmer-class-db-builder-num-cpus	Option to set the number of CPUs available for processing	--kmer-class-db-builder-num-cpus	[1,max avail]
kmer-class-db-builder-num-kmers-per-bucket	Set to output number of kmers in each minimizer bucket. The default value is false.	--kmer-class-db-builder-num-kmers-per-bucket	true/false
kmer-class-db-builder-include-lowercase	Set to include kmers with lowercase bases (usually repeatmasked). The default value is false.	--kmer-class-db-builder-include-lowercase	true/false
kmer-class-db-builder-taxids-as-seq-name	Set to indicate that the reference fastas listed in the input file have taxids as sequence name. In this case, the second column of the input file is ignored. The default value is false.	--kmer-class-db-builder-taxids-as-seq-name	true/false

Targeted Caller Options

Name	Description	Command Line Equivalent	Range
enable-targeted	Enable targeted calling. When the small variant caller is enabled for human germline WGS¹ analysis, then cyp21a2, gba, hba, and rh are enabled by default, otherwise the default is false.	--enable-targeted	true/false or space-separated list of one or more supported target names
targeted-merge-vc	Enable merging of targeted caller small variant VCF records into the <prefix>.hard-filtered.vcf.gz and <prefix>.hard-filtered.gvcf.gz files when the small variant caller is enabled. Enabled by default for cyp21a2, gba, hba, and rh only when sort is enabled.	--targeted-merge-vc	true/false or space-separated list of one or more supported target names
targeted-enable-legacy-output	[DEPRECATED] This option may not be supported for all targets. Enable generation of target-specific .tsv files from previous DRAGEN versions. Default is false.	--targeted-enable-legacy-output	true/false

¹ For exome or enrichment analysis, the default targeted callers are still enabled with the small variant caller, but will not generate any output.