Command Line Option Reference

alt-aware

If alt liftover is used in a hash table, the option enables special processing for alt contigs. If a reference is built with liftover, the option is enabled by default.

--alt-aware

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.

Not applicable

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

Specifies if all lanes of a flow cell are output to the same FASTQ files consecutively. 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 or 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-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.

Not applicable

enable-sampling

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

Not applicable

enable-sort

Enables sorting after mapping/alignment.

Not applicable

enable-variant-caller

Enables the variant caller.

--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.

Not applicable

enable-vcf-indexing

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

Not applicable

fastq-file1

Specifies FASTQ file to input to the DRAGEN pipeline. The GZIP file format is allowed.

-1, --fastq-file1

fastq-file2

Specifies second FASTQ file with paired-end reads toinput.

-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

Enables 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-alt-aware-validate

Disables requirement for a liftover file when building a hash table from a reference that contains alt-contigs.

--ht-alt-aware-validate

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 (B, 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.

--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 (B, 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 decoy 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.

Not applicable

interleaved

Specifies the interleaved paired-end reads in single FASTQ.

-i

intermediate-results-dir

Specifies directory to store intermediate results in (eg, sort partitions).

Not applicable

lic-no-print

Suppresses the license status message at the end of a run.

--lic-no-print

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.

Not applicable

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

Describes 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.

Not applicable

pair-suffix-delimiter

Changes the delimiter character for suffixes.

--pair-suffix-delimiter

preserve-bqsr-tags

Determines whether to preserve BI and BD flags from input BAM file, which can cause problems with hard clipping.

Not applicable

preserve-map-align-order

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

Not applicable

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

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.

Not applicable

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.

Not applicable

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 GZIP format is allowed.

--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 GZIP file format is allowed.

--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-vc

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

Enables use of BAM input files for mapper/aligner.

--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 and affects 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

dedup-min-qual

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

--Aligner.dedup-min-qual

en-alt-hap-aln

Allows chimeric 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 (negative score) for extending a gap.

--Aligner.gap-ext-pen

gap-open-pen

Specifies the penalty (negative score) 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 a reference N nucleotide IUB code.

--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 all secondary alignments cannot 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 beginning or end of the read.

--Aligner.unclip-score

pe-stat-mean-insert

Specifies the average template length.

Not applicable

pe-stat-mean-read-len

Specifies the average read length.

Not applicable

pe-stat-quartiles-insert

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

Not applicable

dn-cnv-vcf

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

Filters joint small variant VCF from the de novo calling step.

--dn-input-vcf

dn-output-vcf

Specifies the file location for writing the filtered VCF file. If not specified, the input VCF is overwritten.

--dn-output-vcf

dn-sv-vcf

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-combinegvcfs

If set to true, DRAGEN combines gVCF run.

--enable-combinegvcfs

enable-joint-genotyping

If set to true, DRAGEN runs the Joint Genotyper.

--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-sv

Enables structural variant caller. The default value is false.

--enable-sv

enable-vlrd

Enables Virtual Long Read Detection.

--enable-vlrd

panel-of-normals

Specifies the path to the panel of normals VCF file.

--panel-of-normals

pedigree-file

Specifies the path to a pedigree file that describes the relationship between panels (specific to joint calling). The pedigree file can contain trios. 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, the option sets the allele frequency call threshold 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, the option sets the allele frequency filter threshold to mark emitted VCF calls as filtered. The default value is 0.05.

--vc-af-filter-threshold

vc-callability-normal-threshold

Specifies the normal sample coverage threshold for a site to be considered callable in the somatic callable regions report.

--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.

--vc-callability-tumor-thresh

vc-decoy-contigs

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

--vc-decoy-contigs

vc-detect-systematic-noise

Specifies the sensitive VCF run mode to use when building a systematic noise file.

--vc-detect-systematic-noise

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 for somatic mode. The default value is false.

--vc-enable-af-filter

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.

--vc-enable-gatk-acceleration

vc-enable-liquid-tumor-mode

Enables liquid tumor mode, which takes account of 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.

--vc-enable-orientation-bias-filter

vc-enable-phasing

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

--vc-enable-phasing

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 true.

--vc-enable-triallelic-filter

vc-enable-vcf-output

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

--vc-enable-vcf-output

vc-forcegt-vcf

Forces genotyping for Germline SNV variant calling. A file (*.vcf or *.vcf.gz) containing a list of small variants is required.

--vc-forcegt-vcf

vc-gvcf-gq-bands

Defines GQ bands for gVCF output. The default value is 10 20 30 40 60 80.

--vc-gvcf-gq-bands

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

Not applicable

vc-max-reads-per-active-region

A down-sampling option that specifies the maximum number of reads for an active region. The default value is 10000.

--vc-max-reads-per-active-region

vc-max-reads-per-active-region-mito

A down-sampling option that 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

A down-sampling option that specifies the maximum number of reads per raw region. The default value is 30000.

--vc-max-reads-per-raw-region

vc-max-reads-per-raw-region-mito

A down-sampling option that 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 for variant calling. The default value is 10.

--vc-min-base-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

A down-sampling option that specifies the minimum number of reads per start position. 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.

Not applicable

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

vc-remove-all-soft-clips

If set to true, the option 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 blocklist BED file.

--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 for both tumor-normal and tumor-only.

--vc-sq-call-threshold

vc-sq-filter-threshold

Sets the SQ filter threshold to mark emitted VCF calls as filtered. The default value is 17.5 for tumor-normal and 6.5 for tumor-only.

--vc-sq-filter-threshold

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-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

vc-target-bed-padding

If needed, pads all of the target BED regions with the specified value. If specified, is used by the small variant caller.

--vc-target-bed-padding

vc-target-coverage

A down-sampling option that specifies the target coverage for small variant calling. The default value is 500 for germline and 50 for somatic mode.

--vc-target-coverage

vc-target-coverage-mito

A down-sampling option that specifies the target coverage for mitochondrial small variant calling. The default value is 40000.

--vc-target-coverage-mito

cnv-blacklist-bed

Specifies regions to blocklist for CNV processing.

--cnv-blacklist-bed

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 counting method for an alignment to be counted in a target bin.

--cnv-counts-method

cnv-enable-gcbias-correction

Enables GC bias correction when performing target counts generation. The default is true.

--cnv-enable-gcbias-correction

cnv-enable-gcbias-smoothing

Enables smoothing of the GC bias correction across adjacent GC bins with an exponential kernel. The default value is true.

--cnv-enable-gcbias-smoothing

cnv-enable-plots

Enables generation of plots. The default value is false.

--cnv-enable-plots

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-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-wgs-interval-width

cnv-matched-normal

Specifies the target counts file of the matched normal sample.

--cnv-matched-normal

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-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-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-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. The default value is 1e–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 10% 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

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. If not specified, 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.

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

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

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

umi-correction-scheme

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

--umi-correction-scheme

umi-correction-table

Enters the path to a customized correction table.

--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

Enters path to target regions file used for UMI on target metrics.

--umi-metrics-interval-file

umi-source

Specifies the input type for the UMI sequence.

--umi-source

umi-fastq

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

--umi-fastq

umi-nonrandom-whitelist

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

--umi-nonrandom-whitelist