General Software Options

alt-aware

Enables special processing for alt contigs, if alt liftover was used in hash table. Enabled by default if reference was built with liftover.

--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.

bam-input

Aligned BAM file for input to the DRAGEN variant caller.

-b, --bam-input

bcl-conversion-only

Perform Illumina BCL conversion to FASTQ format.

--bcl-conversion-only

bcl-input-directory

Input BCL directory for BCL conversion.

--bcl-input-directory

bcl-only-lane

For BCL input, convert only specified lane number (default all lanes).

--bcl-only-lane

sample-sheet

For BCL input, path to SampleSheet.csv file. Default location is the BCL root directory.

--sample-sheet

strict-mode

For BCL input, abort if any files are missing (false by default)

--strict-mode

first-tile-only

Only convert the first tile of each lane during BCL conversion (for testing/debugging)

--first-tile-only

run-info

Set the path to RunInfo.xml file. Default is <flow cell>/RunInfo.xml

--run-info

bcl-sampleproject-subdirectories

For BCL conversion, output to subdirectories based upon sample sheet 'Sample_Project' column

--bcl-sampleproject-subdirectories

no-lane-splitting

Set whether to output all lanes of a flow cell to the same FASTQ files consecutively. Default is false.

--no-lane-splitting

bcl-only-matched-reads

Set whether to output unmapped reads to files marked as Undetermined. Default is false.

bcl-only-matched-reads

bcl-use-hw

Set to false to prevent use of DRAGEN FPGA acceleration during BCL conversion. Default is true.

--bcl-use-hw

bcl-num-parallel-tiles

Number of tiles to process in parallel. Default is dynamically determined.

--bcl-num-parallel-tiles

bcl-num-conversion-threads

Number of conversion threads per tile. Default is dynamically determined.

--bcl-num-conversion-threads

bcl-num-compression-threads

Number of CPU threads for output fastq.gz compression. Default is dynamically determined.

--bcl-num-compression-threads

bcl-num-decompression-threads

Number of CPU threads for BCL input decompression. Default is dynamically determined.

--bcl-num-decompression-threads

shared-thread-odirect-output

Use alternative shared-thread ODIRECT file output. Default is false.

--shared-thread-odirect-output

build-hash-table

Generate a reference/hash table.

--build-hash-table

cram-input

CRAM file for input to the DRAGEN variant caller.

--cram-input

dbsnp

Path to the variant annotation database VCF (or .vcf.gz) file.

--dbsnp

enable-auto-multifile

Import subsequent segments of the *_001.{dbam,fastq} files.

--enable-auto-multifile

enable-bam-indexing

Enable generation of a BAI index file.

--enable-bam-indexing

enable-cnv

Enable copy number variant (CNV).

--enable-cnv

enable-duplicate-marking

Enable the flagging of duplicate output alignment records.

--enable-duplicate-marking

enable-map-align-output

Enables saving the output from the map/align stage. Default is true when only running map/align. Default is false if running the variant caller.

--enable-map-align-output

enable-methylation-calling

Whether to automatically add methylation-tags and output a single BAM for methylation protocols.

enable-sampling

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

enable-sort

Enable sorting after mapping/alignment.

enable-variant-caller

Enables the variant caller.

--enable-variant-caller

enable-vcf-compression

Enable compression of VCF output files. Default is true.

fastq-file1

FASTQ file to input to the DRAGEN pipeline (may be gzipped).

-1, --fastq-file1

fastq-file2

Second FASTQ file with paired-end reads for input.

-2, --fastq-file2

fastq-list

CSV file that contains a list of FASTQ files to process.

--fastq-list

fastq-list-sample-id

Only process entries where the RGSM entry matches the given Sample ID parameter (for fastq-list.csv input).

--fastq-list-sample-id

fastq-list-all-samples

Enable/disable processing of all samples together, regardless of the RGSM value.

--fastq-list-all-samples

fastq-n-quality

Base call quality to output for N bases. Automatically added to fastq-n-quality for all output N’s.

--fastq-n-quality

fastq-offset

FASTQ quality offset value.

--fastq-offset

filter-flags-from-output

Filter output alignments with any bits set in val present in the flags field. Hex and decimal values accepted.

--filter-flags-from-output

force

Force overwrite of existing output file.

-f

force-load-reference

Force loading of the reference and hash tables before starting the DRAGEN pipeline.

-l

generate-md-tags

Whether to generate MD tags with alignment output records. Default is false.

--generate-md-tags

generate-sa-tags

Whether to generate SA:Z tags for records that have chimeric/supplemental alignments.

--generate-sa-tags

generate-zs-tags

Whether to generate ZS tags for alignment output records. Default is false.

--generate-sz-tags

ht-alt-liftover

SAM format liftover file of alternate contigs in reference.

--ht-alt-liftover

ht-pop-alt-contigs

Reference FASTA file with population alternate contigs to augment the standard reference.

--ht-pop-alt-contigs

ht-pop-alt-liftover

SAM format liftover file of population alternate contigs.

--ht-pop-alt-liftover

ht-pop-snps

VCF format file with unphased population SNPs used to augment the standard reference.

--ht-pop-snps

ht-alt-aware-validate

Disable 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

Enable generation of RNA hash table. Default is false.

--ht-build-rna-hashtable

ht-cost-coeff-seed-freq

Cost coefficient of extended seed frequency.

--ht-cost-coeff-seed-freq

ht-cost-coeff-seed-len

Cost coefficient of extended seed length.

--ht-cost-coeff-seed-len

ht-cost-penalty-incr

Cost penalty to incrementally extend a seed another step.

--ht-cost-penalty-incr

ht-cost-penalty

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

Maximum decimation factor for seed thinning.

--ht-max-dec-factor

ht-max-ext-incr

Maximum bases to extend a seed by in one step.

--ht-max-ext-incr

ht-max-ext-seed-len

Maximum extended seed length.

-- ht-max-ext-seed-len

ht-max-seed-freq

Maximum allowed frequency for a seed match after extension attempts.

--ht-max-seed-freq

ht-max-table-chunks

Maximum ~1 GB thread table chunks in memory at once.

--ht-max-table-chunks

ht-mem-limit

Memory limit (hash table + reference), units B|KB|MB|GB.

--ht-mem-limit

ht-methylated

Automatically generate C->T and G->A converted reference hashtables.

--ht-methylated

ht-num-threads

Maximum worker CPU threads for building hash table.

--ht-num-threads

ht-rand-hit-extend

Include a random hit with each EXTEND record of this freq record.

--ht-rand-hit-extend

ht-rand-hit-hifreq

Include a random hit with each HIFREQ record.

--ht-rand-hit-hifreq

ht-ref-seed-interval

Number of positions per reference seed.

--ht-ref-seed-interval

ht-reference

Reference file in .fasta format to be used to build a hash table.

--ht-reference

ht-seed-len

Initial seed length to store in hash table.

--ht-seed-len

ht-size

Size of hash table, units B|KB|MB|GB.

--ht-size

ht-soft-seed-freq-cap

Soft seed frequency cap for thinning

--ht-soft-seed-freq-cap

ht-suppress-decoys

Suppress the use of a decoys file when building a hash table.

--ht-suppress-decoys

ht-target-seed-freq

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.

interleaved

Interleaved paired-end reads in single FASTQ.

-i

intermediate-results-dir

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

lic-no-print

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

--lic-no-print

methylation-generate-cytosine-report

Generate a genomewide cytosine methylation report.

--methylation-generate-cytosine-report

methylation-generate-mbias-report

Generate a per-sequencer-cycle methylation bias report.

methylation-TAPS

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

--methylation-TAPS

methylation-match-bismark

If true, match bismark’s tags exactly, including bugs.

--methylation-match-bismark

methylation-protocol

Library protocol for methylation analysis.

--methylation-protocol

num-threads

The number of processor threads to use.

-n, --num-threads

output-directory

Output directory.

--output-directory

output-file-prefix

Output file name prefix to use for all files generated by the pipeline.

--output-file-prefix

output-format

The format of the output file from the map/align stage. Valid values are bam (the default), sam, or dbam (a proprietary binary format).

--output-format

pair-by-name

Whether to shuffle the order of BAM input records such that paired-end mates are processed together.

pair-suffix-delimiter

Change the delimiter character for suffixes.

--pair-suffix-delimiter

preserve-bqsr-tags

Whether to preserve input BAM file’s BI and BD flags. Note this may cause problems with hard clipping.

preserve-map-align-order

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

qc-coverage-region-1

First bed file to report coverage on.

--qc-coverage-region-1

qc-coverage-region-2

Second bed file to report coverage on.

--qc-coverage-region-2

qc-coverage-region-3

Third bed file to report coverage on.

--qc-coverage-region-3

qc-coverage-reports-1

Types of reports requested for qc-coverage-region-1.

--qc-coverage-reports-1

qc-coverage-reports-2

Types of reports requested for qc-coverage-region-2.

--qc-coverage-reports-2

qc-coverage-reports-3

Types of reports requested for qc-coverage-region-3.

--qc-coverage-reports-3

ref-dir

Directory containing the reference hash table. This reference is automatically loaded to the DRAGEN card, if it is not already there.

-r, --ref-dir

ref-sequence-filter

Output only reads mapping to this reference sequence.

--ref-sequence-filter

remove-duplicates

If true, remove duplicate alignment records instead of just flagging them.

RGCN

Read group sequencing center name.

--RGCN

RGCN-tumor

Read group sequencing center name for tumor input.

--RGCN-tumor

RGDS

Read group description.

--RGDS

RGDS-tumor

Read group description for tumor input.

--RGDS-tumor

RGDT

Read group run date.

--RGDT

RGDT-tumor

Read group run date for tumor input.

--RGDT-tumor

RGID

Read group ID.

--RGID

RGID-tumor

Read group ID for tumor input.

--RGID-tumor

RGLB

Read group library.

--RGLB

RGLB-tumor

Read group library for tumor input.

--RGLB-tumor

RGPI

Read group predicted insert size.

--RGPI

RGPI-tumor

Read group predicted insert size for tumor input.

--RGPI-tumor

RGPL

Read group sequencing technology.

--RGPL

RGPL-tumor

Read group sequencing technology for tumor input.

--RGPL-tumor

RGPU

Read group platform unit.

--RGPU

RGPU-tumor

Read group platform unit for tumor input.

--RGPU-tumor

RGSM

Read group sample name.

--RGSM

RGSM-tumor

Read group sample name for tumor input.

--RGSM-tumor

sample-size

Number of reads to sample when enable-sampling is true.

sample-sex

Sex of the sample.

--sample-sex

strip-input-qname-suffixes

Whether to strip read-index suffixes (eg, /1 and /2) from input QNAMEs.

tumor-bam-input

Aligned BAM file for the DRAGEN variant caller in somatic mode.

--tumor-bam-input

tumor-cram-input

Aligned CRAM file for the DRAGEN variant caller in somatic mode.

--tumor-cram-input

tumor-fastq-list

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

The sample ID for the list of FASTQ files specified by tumor-fastq-list.

--tumor-fastq-list-sample-id

tumor-fastq1

FASTQ file for the DRAGEN pipeline using the variant caller in somatic mode (may be gzipped).

--tumor-fastq1

tumor-fastq2

Second FASTQ file with reads paired to tumor-fastq1 reads for the DRAGEN pipeline using the variant caller in somatic mode (may be gzipped).

--tumor-fastq2

verbose

Enable verbose output from DRAGEN.

-v