Command-Line Options

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

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

bcl-conversion-only

Performs Illumina BCL conversion to FASTQ format.

--bcl-conversion-only

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

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

first-tile-only

Converts only the first tile of each lane during BCL conversion. Use for testing or debugging.

--first-tile-only

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

bcl-only-matched-reads

Specifies if unmapped reads are output to files marked as Undetermined. The default value is false.

bcl-only-matched-reads

bcl-use-hw

If set to false, the option prevents DRAGEN FPGA acceleration during BCL conversion. The default value is true.

--bcl-use-hw

bcl-num-parallel-tiles

Specifies the number of tiles to process in parallel. The default value is dynamically determined.

--bcl-num-parallel-tiles

bcl-num-conversion-threads

Specifies the number of conversion threads per tile. The default value is dynamically determined.

--bcl-num-conversion-threads

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

bcl-num-decompression-threads

Specifies the number of CPU threads for BCL input decompression. The default value is dynamically determined.

--bcl-num-decompression-threads

shared-thread-odirect-output

Uses alternative shared-thread ODIRECT file output. The default value is false.

--shared-thread-odirect-output

build-hash-table

Generates a reference hash table.

--build-hash-table

cram-input

Specifies the CRAM file input for the DRAGEN variant caller.

--cram-input

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

enable-bam-indexing

Enables generation of a BAI index file.

--enable-bam-indexing

enable-cram-indexing

Enables generation of a CRAI index file.

--enable-cram-indexing

enable-cnv

Enables copy number variant (CNV).

--enable-cnv

enable-duplicate-marking

Enables the flagging of duplicate output alignment records.

--enable-duplicate-marking

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

enable-methylation-calling

Automatically adds tags related to methylation and outputs a single BAM for methylation protocols.

--enable-methylation-calling

enable-sampling

Automatically detects paired-end parameters by running a sample through the mapper/aligner.

--enable-sampling

enable-sort

Enables sorting after mapping/alignment.

--enable-sort

enable-variant-caller

Enables the variant caller.(default=false)

--enable-variant-caller

enable-variant-deduplication

Enables variant deduplication. The default value is false.

--enable-variant-deduplication

enable-vcf-compression

Enables compression of VCF output files. The default value is true.

--enable-vcf-compression

enable-vcf-indexing

Outputs a *.tbi index file in addition to the output VCF/gVCF. The default is true.

--enable-vcf-indexing

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-all-samples

Disables processing of all samples together, regardless of the RGSM value.

--fastq-list-all-samples

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

fastq-offset

Sets the FASTQ quality offset value.

--fastq-offset

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

generate-sa-tags

Generates SA:Z tags for records that have chimeric or supplemental alignments.

--generate-sa-tags

generate-zs-tags

Generate ZS tags for alignment output records. The default value is false.

--generate-sz-tags

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

ht-build-rna-hashtable

Enables generation of RNA hash table. The default value is false.

--ht-build-rna-hashtable

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

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

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

lic-server

Specifies the license server for cloud sites:
http://<base64_use>:<base64_password>@<path to server>

--lic-server

lic-instance-id-location

Use this option to override the default cloud instance ID location

--lic-instance-id-location

methylation-generate-cytosine-report

Generates a genome-wide cytosine methylation report.

--methylation-generate-cytosine-report

methylation-generate-mbias-report

Generates a per system cycle methylation bias report.

--methylation-generate-mbias-report

methylation-TAPS

If input assays are generated by TAPS, the option is set to true.

--methylation-TAPS

methylation-match-bismark

If true, the option matches Bismark tags exactly, including bugs.

--methylation-match-bismark

methylation-protocol

Describes library protocol for methylation analysis.

--methylation-protocol

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

--output-format

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

preserve-map-align-order

Produces output file that preserves original order of reads in the input file.

--preserve-map-align-order

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

qc-coverage-reports-2

Describes the types of reports requested for qc-coverage-region-2.

--qc-coverage-reports-2

qc-coverage-reports-3

Describes the types of reports requested for qc-coverage-region-3.

--qc-coverage-reports-3

qc-coverage-region-1-thresholds

Declares the thresholds to use in cov_report for qc-coverage-region-1.

--qc-coverage-region-1-thresholds

qc-coverage-region-2-thresholds

Declares the thresholds to use in cov_report for qc-coverage-region-2.

--qc-coverage-region-2-thresholds

qc-coverage-region-3-thresholds

Declares the thresholds to use in cov_report for qc-coverage-region-3.

--qc-coverage-reports-3

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.

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

tumor-bam-input

Specifies aligned BAM file for the DRAGEN variant caller in somatic mode.

--tumor-bam-input

tumor-cram-input

Specifies aligned CRAM file for the DRAGEN variant caller in somatic mode.

--tumor-cram-input

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

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

ann-sj-max-indel

Specifies maximum indel length to expect near an annotated splice junction.

--Mapper.ann-sj-max-indel

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-mode

Controls when seed editing is used. The following values represent the different edit modes:

--Mapper.edit-mode

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-seed-num

For edit-mode 1 or 2, controls the requested number of seeds per read to allow editing on.

--Mapper.edit-seed-num

enable-map-align

Enable the mapper/aligner (Default=true)

--enable-map-align

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):

--Mapper.map-orientations

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

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

clip-pe-overhang

When set to a nonzero value, clips 3 read ends overhanging their mate's 5 ends as aligned. The following values represent the different options:

--Aligner.clip-pe-overhang

dedup-min-qual

Specifies a minimum base quality for calculating read quality metric for deduplication.

--Aligner.dedup-min-qual

en-alt-hap-aln

Allows haplotype alignments to be output as supplementary.

--Aligner.en-alt-hap-aln

en-chimeric-aln

Allows chimeric alignments to be output as supplementary.

--Aligner.en-chimeric-aln

gap-ext-pen

Specifies the penalty for extending a gap.

--Aligner.gap-ext-pen

gap-open-pen

Specifies the penalty for opening a gap (ie, insertion or deletion).

gap-open-pen

global

Controls whether alignment is end-to-end in the read. The following values represent the different alignments:

--Aligner.global

hard-clips

Specifies alignments for hard clipping. The following values represent the different alignments:

--Aligner.hard-clips

map-orientations

Constrains orientations to accept forward-only, reverse-complement only, or any alignments. The following values represent the different orientations:

--Aligner.map-orientations

mapq-max

Specifies ceiling on reported MAPQ. The default value is 60.

--Aligner.mapq-max

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

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

match-score

Specifies the score increment for matching reference nucleotide.

--Aligner.match-score

max-rescues

Specifies maximum rescue alignments per read pair. The default value is 10.

--max-rescues

min-score-coeff

Sets adjustment to aln-min-score per read base.

--Aligner.min-score-coeff

mismatch-pen

Defines the score penalty for a mismatch.

--Aligner.mismatch-pen

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

no-unpaired

Determines if only properly paired alignments should be reported for paired reads.

--Aligner. no-unpaired

pe-max-penalty

Specifies the maximum pairing score penalty for unpaired or distant ends.

--Aligner.pe-max-penalty

pe-orientation

Specifies the expected paired-end orientation. The following values represent the different orientations:

--Aligner.pe-orientation

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

sec-aligns-hard

If set to 1, forces the read to be unmapped when not all secondary alignments be output.

--Aligner.sec-aligns-hard

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

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

supp-as-sec

Determines if supplementary alignments should be reported with secondary flag.

--Aligner.supp-as-sec

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

pe-stat-mean-insert

Specifies the average template length.

--pe-stat-mean-insert

pe-stat-mean-read-len

Specifies the average read length.

--pe-stat-mean-read-len

pe-stat-quartiles-insert

Specifies a comma-delimited trio of numbers for the 25^th, 50^th, and 75^th percentile template lengths.

--pe-stat-quartiles-insert

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

enable-multi-sample-gvcf

Enables generation of a multisample gVCF file. If set to true, DRAGEN requires a combined gVCF file as input.

--enable-multi-sample-gvcf

enable-vlrd

Enables Virtual Long Read Detection.

--enable-vlrd

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 value 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 value is 50.

--vc-callability-tumor-thresh

vc-decoy-contigs

Specifies the path to a comma-separated list of contigs to skip during variant calling.

--vc-depth-annotation-threshold

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-filter-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-decoy-contigs

vc-emit-ref-confidence

Enables base pair resolution gVCF generation or banded gVCF generation.

--vc-emit-ref-confidence

vc-enable-af-filter

Enables the allele frequency filter of nuclear chromosomes for somatic mode. The default value is false.

--vc-enable-af-filter

vc-enable-af-filter-mito

Enables the allele frequency filter for mitochondrial variant calling. The default value is true.

--vc-enable-af-filter-mito

vc-enable-baf

Enables B-allele frequency output. The default value is true.

--vc-enable-baf

vc-enable-decoy-contigs

Enables variant calls on decoy contigs. The default value is false.

--vc-enable-decoy-contigs

vc-enable-gatk-acceleration

Enables running variant caller in GATK mode. The default value is false.

--vc-enable-gatk-acceleration

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

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

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

vc-enable-phasing

Enables variants to be phased when possible. The default value is true.

--vc-enable-phasing

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 default value is 0, which disables the option.

--vc-combine-phased-variants-distance

vc-detect-systematic-noise

Enables a sensitive run mode for building a systematic noise file from normal samples. The mode is not intended for analyzing tumor samples. The default value is false.

--vc-detect-systematic-noise

vc-enable-roh

Enables the ROH caller and output. The default value is true.

--vc-enable-roh

vc-enable-triallelic-filter

Enables the multiallelic filter for somatic mode. The default value is false.

--vc-enable-triallelic-filter

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

vc-enable-vcf-output

Enables VCF file output during a gVCF run. The default value is false.

--vc-enable-vcf-output

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

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

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

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

DRAGENHardQUAL:all: QUAL < 10.4139;LowDepth:all: DP < 1

--vc-hard-filter

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

vc-min-contig-qual

Specifies the minimum base quality to be considered for De Bruijn graph construction. The default value is 10.

--vc-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:

--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-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

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

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-target-bed

If provided, the variant caller only outputs variants with a reference position that overlaps with any of the regions in the target BED.

--vc-target-bed

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-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

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

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

germline-tagging-db-threshold

The minimum alternative allele count in population database for a variant to be defined as germline. The default value is 100.

--germline-tagging-db-threshold

enable-maf-output

Enables Mutation Annotation Format (MAF) output. The default value is false.

--enable-maf-output

maf-transcript-source

Specifies desired transcript source for Mutation Annotation Format (MAF) output.

--maf-transcript-source

maf-input-vcf

Specifies input VCF file for standalone Mutation Annotation Format (MAF) output.

--maf-input-vcf

cnv-exclude-bed

Specifies regions to exclude from 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

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

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

cnv-enable-gcbias-correction

Enables GC bias correction. The default is true.

--cnv-enable-gcbias-correction

cnv-enable-gcbias-smoothing

Enables smoothing across GC bins. The default value is true.

--cnv-enable-gcbias-smoothing

cnv-enable-gender-matched-pon

Enable gender matched PON normalization. The default value is true.

--cnv-enable-gender-matched-pon

cnv-enable-ref-calls

When set to true, copy neutral (REF) calls are included in the output VCF.

--cnv-enable-ref-calls

cnv-enable-self-normalization

Enables self-normalization.

--cnv-enable-self-normalization

cnv-enable-tracks

Enables generation of track files that can be imported into IGV for viewing. The default is true.

--cnv-enable-tracks

cnv-extreme-percentile

Specifies the extreme median percentile value used to filter out samples. The default value is 2.5.

--cnv-extreme-percentile

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

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

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

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

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

cnv-filter-qual

Specifies the QUAL value at which a reported event is marked as PASS in the output VCF file.

--cnv-filter-qual

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

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

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

cnv-merge-distance

Specifies the maximum segment gap allowed for merging segments.

--cnv-merge-distance

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

cnv-min-mapq

Specifies the minimum MAPQ for alignment to be counted.

--cnv-min-mapq

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

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

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-allel-vcf

CNV population SNP input VCF file.

--cnv-population-b-allel-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

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

cnv-segmentation-mode

Specifies the segmentation algorithm to perform.

--cnv-segmentation-mode

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

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

cnv-slm-stepeta

Specifies the distance normalization parameter. The default value is 10000. Only valid for HSLM.

--cnv-slm-stepeta

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

vc-systematic-noise-raw-input-list

Generates a list of VCFs to be used. One VCF per line.

--vc-systematic-noise-raw-input-list

vc-systematic-noise-germline-vaf-threshold

Specifies the minimal variant allele frequency to remove potential germlines from the systematic noise file building. The default is unspecified, which indicates that all variants are used.

--vc-systematic-noise-germline-vaf-threshold

vc-systematic-noise-use-germline-tag

Determines whether to use DRAGEN internal germline tagging to remove potential germlines. Mutually exclusive with --vc-systematic-noise-germline-vaf-threshold. The default value is false. DRAGEN recommends setting this option to true for WGS analysis.

--vc-systematic-noise-use-germline-tag

vc-systematic-noise-method

Describes the method used to calculate the systematic noise level across samples. The default method is mean.

--vc-systematic-noise-method

enable-sv

Enables the structural variant caller. The default value is false.

--enable-sv

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

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.

--sv-exome

sv-output-contigs

Set to true to have assembled contig sequences output in a VCF file. The default value is false.

--sv-output-contigs

enable

Enables repeat expansion detection.

--repeat-genotype-enable

specs

Specifies the full path to the JSON file that contains the repeat variant catalog (specification) describing the loci to call.

--repeat-genotype-specs

enable-rna

Enables processing of RNA-seq data.

--enable-rna

annotation-file

Use to supply a gene annotation file. Required for quantification and gene-fusion.

--annotation-file, -a

enable-rna-quantification

Enables RNA quantification.

--enable-rna-quantification

rna-quantification-library-type

Specifies the type of the RNA-seq library. The default value is autodetect.

--rna-quantification-library-type

rna-quantification-gc-bias

Enables correction for GC bias in fragment counts.

--rna-quantification-gc-bias

enable-rna-gene-fusion

Enables RNA gene fusion calling.

--enable-rna-gene-fusion

umi-library-type

Sets the batch option for correcting UMIs. Not required.

--umi-library-type

umi-enable

Enables UMI-based read processing.

--umi-enable

vc-enable-umi-solid

Enables solid tumor UMI-aware VC settings. The default value is false.

--vc-enable-umi-solid

vc-enable-umi-liquid

Enables liquid tumor UMI-aware VC settings. The default value is false.

--vc-enable-umi-liquid

vc-enable-umi-germline

Allow germline VC from UMI-collapsed reads. The default value is false.

--vc-enable-umi-germline

umi-correction-scheme

Describes the methodology to use for correcting sequencing errors in UMIs.

--umi-correction-scheme

umi-correction-table

Provides the path to the correction table for lookup correction scheme.

--umi-correction-table

umi-emit-multiplicity

Sets the consensus read output type.

--umi-emit-multiplicity

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

umi-metrics-interval-file

Provides the path to target regions file used for UMI on target metrics.

--umi-metrics-interval-file

umi-source

Specifies the location to read UMIs from.

--umi-source

umi-fastq

Provides the path to a separate FASTQ file with UMI sequences for each read.

--umi-fastq

umi-nonrandom-whitelist

Provides the path to a file containing valid nonrandom UMIs sequences. Enter one path per line.

--umi-nonrandom-whitelist