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.
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 |
|---|---|---|---|
The following options are in the [Mapper] section of the configuration file. For more detailed information on these options, see [DNA Mapping]{.underline}.
The following options are in the [Aligner] section of the configuration file. For more information, see [DNA Aligning]{.underline}
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.
The following options are in the Variant Caller section of the configuration file. For more information on these options, see [Variant Caller Options]{.underline}.
The following options are applicable to the CNV caller.
The following options pertain to the VNTR Caller. For more information on these options, see the VNTR Calling page.
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}.
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.
Step 2. Generate the final noise file with:
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).
¹ For exome or enrichment analysis, the default targeted callers are still enabled with the small variant caller, but will not generate any output.
| Name | Description | Command Line Equivalent | Range |
|---|---|---|---|
| Name | Description | Command Line Equivalent | Value |
|---|---|---|---|
| Option | Description | Command Line Equivalent | Value |
|---|---|---|---|
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|---|---|---|---|
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| Name | Description | Command Line Equivalent | Range |
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| Name | Description | Command Line Equivalent | Range |
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| 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
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
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
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
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
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
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-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
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.
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
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
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)
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-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
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
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
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]
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]
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
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