dragen-somatic-with-germline-pipeline/4.2.4__20240830041201

Overview

MD5Sum: a9d59f7474a1b87d531c2a859a29316d

Documentation

Documentation for dragen-somatic-with-germline-pipeline
v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_2_4__20240830041201 / Bundle Version v9_r3__20240830041201

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240830041201.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3

Bundle ID: 1288012a-b0dd-4ccd-bc2a-576fad2f7f0d

• Bundle Link
  Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
  Pipeline Project Name: pipelines
  Pipeline ID: 0f5575bc-6cf8-4a90-a80e-05088aae8ed7
  Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240830041201

Projects

• development
• staging

Datasets

• dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
• wgs_validation_fastq__cups_pair_8
• wgs_validation_fastq__2016_249_17_MH_P033
• wgs_validation_fastq__2016_249_18_WH_P025
• wgs_validation_fastq__B_ALL_Case_10
• wgs_validation_fastq_Diploid_Never_Responder
• wgs_validation_fastq_SBJ00303
• wgs_validation_fastq_SEQC50
• wgs_validation_fastq_SFRC01073

Bundle Name: dragen_somatic_with_germline_pipeline_prod__4_2_4__20240830041201 / Bundle Version v9_r3__20240830041201

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240830041201.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3

Bundle ID: 71297be1-5180-4f64-ac0e-2846a0a51e56

• Bundle Link
  Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
  Pipeline Project Name: pipelines
  Pipeline ID: 0f5575bc-6cf8-4a90-a80e-05088aae8ed7
  Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240830041201

Projects

• production

Datasets

• dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna

Visual Overview

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Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-somatic-with-germline-pipeline%2F4.2.4__20240830041201/dragen-somatic-with-germline-pipeline__4.2.4__20240830041201.schema.json

# bam input (Optional)
# Docs: Input a normal BAM file for the variant calling stage
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# cnv enable self normalization (Optional)
# Docs: Enable CNV self normalization.
# Self Normalization requires that the DRAGEN hash table be generated with the enable-cnv=true option.
cnv_enable_self_normalization: false

# cnv normal b allele vcf (Optional)
# Docs: Specify a matched normal SNV VCF.
cnv_normal_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv normal cnv vcf (Optional)
# Docs: Specify germline CNVs from the matched normal sample.
cnv_normal_cnv_vcf: false

# cnv population b allele vcf (Optional)
# Docs: Specify a population SNP catalog.
cnv_population_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv somatic enable het calling (Optional)
# Docs: Enable HET-calling mode for heterogeneous segments.
cnv_somatic_enable_het_calling: false

# cnv somatic enable lower ploidy limit (Optional)
# Docs: To improve accuracy on the tumor ploidy model estimation, the somatic WGS CNV caller estimates whether the chosen model calls 
# homozygous deletions on regions that are likely to reduce the overall fitness of cells, 
# which are therefore deemed to be "essential" and under negative selection. 
# In the current literature, recent efforts tried to map such cell-essential genes (eg, in 2015 - https://www.science.org/doi/10.1126/science.aac7041).
# The check on essential regions is controlled with --cnv-somatic-enable-lower-ploidy-limit (default true).
cnv_somatic_enable_lower_ploidy_limit: false

# cnv somatic essential genes bed (Optional)
# Docs: Default bedfiles describing the essential regions are provided for hg19, GRCh37, hs37d5, GRCh38, 
# but a custom bedfile can also be provided in input through the 
# --cnv-somatic-essential-genes-bed=<BEDFILE_PATH> parameter. 
# In such case, the feature is automatically enabled. 
# A custom essential regions bedfile needs to have the following format: 4-column, tab-separated, 
# where the first 3 columns identify the coordinates of the essential region (chromosome, 0-based start, excluded end). 
# The fourth column is the region id (string type). For the purpose of the algorithm, currently only the first 3 columns are used. 
# However, the fourth might be helpful to investigate manually which regions drove the decisions on model plausibility made by the caller.
cnv_somatic_essential_genes_bed: string

# cnv use somatic vc baf (Optional)
# Docs: If running in tumor-normal mode with the SNV caller enabled, use this option
# to specify the germline heterozygous sites.
cnv_use_somatic_vc_baf: false

# cnv use somatic vc vaf (Optional)
# Docs: Use the variant allele frequencies (VAFs) from the somatic SNVs to help select
# the tumor model for the sample.
cnv_use_somatic_vc_vaf: false

# cram input (Optional)
# Docs: Input a normal CRAM file for the variant calling stage
cram_input:
  class: File
  location: icav2://project_id/path/to/file

# cram reference (Optional)
# Docs: Path to the reference fasta file for the CRAM input. 
# Required only if the input is a cram file AND not the reference in the tarball
cram_reference:
  class: File
  location: icav2://project_id/path/to/file

# dbsnp annotation (Optional)
# Docs: In Germline, Tumor-Normal somatic, or Tumor-Only somatic modes,
# DRAGEN can look up variant calls in a dbSNP database and add annotations for any matches that it finds there.
# To enable the dbSNP database search, set the --dbsnp option to the full path to the dbSNP database
# VCF or .vcf.gz file, which must be sorted in reference order.
dbsnp_annotation:
  class: File
  location: icav2://project_id/path/to/file

# deduplicate minimum quality (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual: string

# deduplicate minimum quality germline (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_germline: string

# deduplicate minimum quality somatic (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_somatic: string

# enable cnv calling (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software.
enable_cnv: false

# enable duplicate marking (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking: false

# enable duplicate marking germline (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_germline: false

# enable duplicate marking somatic (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_somatic: false

# enable hla (Optional)
# Docs: Enable HLA typing by setting --enable-hla flag to true
enable_hla: false

# enable hrd (Optional)
# Docs: Set to true to enable HRD scoring to quantify genomic instability.
# Requires somatic CNV calls.
enable_hrd: false

# enable map align (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align: false

# enable map align germline (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align_germline: false

# enable map align output (Optional)
# Docs: 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: false

# enable map align output germline (Optional)
# Docs: 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_germline: false

# enable map align output somatic (Optional)
# Docs: 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_somatic: false

# enable map align somatic (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align_somatic: false

# enable rna (Optional)
# Docs: Set this option for running RNA samples through T/N workflow
enable_rna: false

# enable sort (Optional)
# Docs: True by default, only set this to false if using --bam-input parameter
enable_sort: false

# enable sort germline (Optional)
# Docs: True by default, only set this to false if using --bam-input parameter
enable_sort_germline: false

# enable sort somatic (Optional)
# Docs: True by default, only set this to false if using --bam-input parameter
enable_sort_somatic: false

# enable sv (Optional)
# Docs: Enable/disable structural variant
# caller. Default is false.
enable_sv: false

# enable sv germline (Optional)
# Docs: Enable/disable structural variant
# caller. Default is false.
enable_sv_germline: false

# enable sv somatic (Optional)
# Docs: Enable/disable structural variant
# caller. Default is false.
enable_sv_somatic: false

# enable tmb (Optional)
# Docs: Enables TMB. If set, the small variant caller, Illumina Annotation Engine,
# and the related callability report are enabled.
enable_tmb: false

# fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files for normal sample
# to process.
fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# hla allele frequency file (Optional)
# Docs: Use the population-level HLA allele frequency file to break ties if one or more HLA allele produces the same or similar results.
# The input HLA allele frequency file must be in CSV format and contain the HLA alleles and the occurrence frequency in population.
# If --hla-allele-frequency-file is not specified, DRAGEN automatically uses hla_classI_allele_frequency.csv from /opt/edico/config/.
# Population-level allele frequencies can be obtained from the Allele Frequency Net database.
hla_allele_frequency_file:
  class: File
  location: icav2://project_id/path/to/file

# hla bed file (Optional)
# Docs: Use the HLA region BED input file to specify the region to extract HLA reads from.
# DRAGEN HLA Caller parses the input file for regions within the BED file, and then
# extracts reads accordingly to align with the HLA allele reference.
hla_bed_file:
  class: File
  location: icav2://project_id/path/to/file

# hla min reads (Optional)
# Docs: Set the minimum number of reads to align to HLA alleles to ensure sufficient coverage and perform HLA typing.
# The default value is 1000 and suggested for WES samples. If using samples with less coverage, you can use a
# lower threshold value.
hla_min_reads: string

# hla reference file (Optional)
# Docs: Use the HLA allele reference file to specify the reference alleles to align against.
# The input HLA reference file must be in FASTA format and contain the protein sequence separated into exons.
# If --hla-reference-file is not specified, DRAGEN uses hla_classI_ref_freq.fasta from /opt/edico/config/.
# The reference HLA sequences are obtained from the IMGT/HLA database.
hla_reference_file:
  class: File
  location: icav2://project_id/path/to/file

# hla tiebreaker threshold (Optional)
# Docs: If more than one allele has a similar number of reads aligned and there is not a clear indicator for the best allele,
# the alleles are considered as ties. The HLA Caller places the tied alleles into a candidate set for tie breaking based
# on the population allele frequency. If an allele has more than the specified fraction of reads aligned (normalized to
# the top hit), then the allele is included into the candidate set for tie breaking. The default value is 0.97.
hla_tiebreaker_threshold: string

# hla zygosity threshold (Optional)
# Docs: If the minor allele at a given locus has fewer reads mapped than a fraction of the read count of the major allele,
# then the HLA Caller infers homozygosity for the given HLA-I gene. You can use this option to specify the fraction value.
# The default value is 0.15.
hla_zygosity_threshold: string

# license instance id location (Optional)
# Default value: /opt/instance-identity
# Docs: You may wish to place your own in.
# Optional value, default set to /opt/instance-identity
# which is a path inside the dragen container
lic_instance_id_location:
  class: File
  location: icav2://project_id/path/to/file

# output prefix germline (Required)
# Docs: The prefix given to all outputs for the dragen germline pipeline
output_prefix_germline: string

# output prefix somatic (Required)
# Docs: The prefix given to all outputs for the dragen somatic pipeline
output_prefix_somatic: string

# qc coverage ignore overlaps (Optional)
# Docs: Set to true to resolve all of the alignments for each fragment and avoid double-counting any
# overlapping bases. This might result in marginally longer run times.
# This option also requires setting --enable-map-align=true.
qc_coverage_ignore_overlaps: false

# qc coverage region 1 (Optional)
# Docs: Generates coverage region report using bed file 1.
qc_coverage_region_1:
  class: File
  location: icav2://project_id/path/to/file

# qc coverage region 2 (Optional)
# Docs: Generates coverage region report using bed file 2.
qc_coverage_region_2:
  class: File
  location: icav2://project_id/path/to/file

# qc coverage region 3 (Optional)
# Docs: Generates coverage region report using bed file 3.
qc_coverage_region_3:
  class: File
  location: icav2://project_id/path/to/file

# reference tar (Required)
# Docs: Path to ref data tarball
reference_tar:
  class: File
  location: icav2://project_id/path/to/file

# repeat genotype enable (Optional)
# Docs: Enables repeat expansion detection.
repeat_genotype_enable: false

# repeat genotype specs (Optional)
# Docs: Specifies the full path to the JSON file that contains the
# repeat variant catalog (specification) describing the loci to call.
# If the option is not provided, DRAGEN attempts to autodetect the applicable catalog file
# from /opt/edico/repeat-specs/ based on the reference provided.
repeat_genotype_specs:
  class: File
  location: icav2://project_id/path/to/file

# repeat genotype use catalog (Optional)
# Docs: 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

# sample sex (Optional)
# Docs: Specifies the sex of a sample
sample_sex: male

# sv call regions bed (Optional)
# Docs: Specifies a BED file containing the set of regions to call.
sv_call_regions_bed:
  class: File
  location: icav2://project_id/path/to/file

# sv discovery (Optional)
# Docs: Enable SV discovery. This flag can be set to false only when --sv-forcegt-vcf is used.
# When set to false, SV discovery is disabled and only the forced genotyping input variants
# are processed. The default is true.
sv_discovery: false

# sv enable liquid tumor mode (Optional)
# Docs: Enable liquid tumor mode.
sv_enable_liquid_tumor_mode: false

# sv enable somatic ins tandup hotspot regions (Optional)
# Docs: Enable or disable the ITD hotspot region input. The default is true in somatic variant analysis.
sv_enable_somatic_ins_tandup_hotspot_regions: false

# sv exome (Optional)
# Docs: Set to true to configure the variant caller for targeted sequencing inputs,
# which includes disabling high depth filters.
# In integrated mode, the default is to autodetect targeted sequencing input,
# and in standalone mode the default is false.
sv_exome: false

# sv forcegt vcf (Optional)
# Docs: Specify a VCF of structural variants for forced genotyping. The variants are scored and emitted
# 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:
  class: File
  location: icav2://project_id/path/to/file

# sv output contigs (Optional)
# Docs: Set to true to have assembled contig sequences output in a VCF file. The default is false.
sv_output_contigs: false

# sv region (Optional)
# Docs: Limit the analysis to a specified region of the genome for debugging purposes.
# This option can be specified multiple times to build a list of regions.
# The value must be in the format "chr:startPos-endPos"..
sv_region: string

# sv use overlap pair evidence (Optional)
# Docs: Allow overlapping read pairs to be considered as evidence.
# By default, DRAGEN uses autodetect on the fraction of overlapping read pairs if <20%.
sv_se_overlap_pair_evidence: false

# sv somatic ins tandup hotspot regions bed (Optional)
# Docs: Specify a BED of ITD hotspot regions to increase sensitivity for calling ITDs in somatic variant analysis.
# By default, DRAGEN SV automatically selects areference-specific hotspots BED file from
# /opt/edico/config/sv_somatic_ins_tandup_hotspot_*.bed.
sv_somatic_ins_tandup_hotspot_regions_bed:
  class: File
  location: icav2://project_id/path/to/file

# sv tin contam tolerance (Optional)
# Docs: Set the Tumor-in-Normal (TiN) contamination tolerance level.
# You can enter any value between 0-1. The default maximum TiN contamination tolerance is 0.15.
sv_tin_contam_tolerance: string

# tmb db threshold (Optional)
# Docs: Specify the minimum allele count (total number of observations) for an allele in gnomAD or 1000 Genome
# to be considered a germline variant.  Variant calls that have the same positions and allele are ignored
# from the TMB calculation. The default value is 10.
tmb_db_threshold: string

# tmb vaf threshold (Optional)
# Docs: Specify the minimum VAF threshold for a variant. Variants that do not meet the threshold are filtered out.
# The default value is 0.05.
tmb_vaf_threshold: string

# tumor bam input (Optional)
# Docs: Input a tumor BAM file for the variant calling stage
tumor_bam_input:
  class: File
  location: icav2://project_id/path/to/file

# tumor cram input (Optional)
# Docs: Input a tumor CRAM file for the variant calling stage
tumor_cram_input:
  class: File
  location: icav2://project_id/path/to/file

# tumor fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files
# to process.
tumor_fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
tumor_fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# vc af call threshold (Optional)
# Docs: Set the allele frequency call threshold to emit a call in the VCF if the AF filter is enabled.
# The default is 0.01.
vc_af_call_threshold: string

# vc af call threshold mito (Optional)
# Docs: 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: false

# vc af filter threshold (Optional)
# Docs: Set the allele frequency filter threshold to mark emitted VCF calls as filtered if the AF filter is
# enabled.
# The default is 0.05.
vc_af_filter_threshold: string

# vc af filter threshold mito (Optional)
# Docs: 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: string

# vc base qual threshold (Optional)
# Docs: (Replaces --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_base_qual_threshold: string

# vc base qual threshold germline (Optional)
# Docs: (Replaces --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_base_qual_threshold_germline: string

# vc base qual threshold somatic (Optional)
# Docs: (Replaces --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_base_qual_threshold_somatic: string

# vc callability normal thresh (Optional)
# Docs: The --vc-callability-normal-thresh option specifies the callability threshold for normal samples.
# The somatic callable regions report includes all regions with normal coverage above the normal threshold.
vc_callability_normal_thresh: string

# vc callability tumor thresh (Optional)
# Docs: The --vc-callability-tumor-thresh option specifies the callability threshold for tumor samples. The
# somatic callable regions report includes all regions with tumor coverage above the tumor threshold.
vc_callability_tumor_thresh: string

# vc combine phased variants distance somatic (Optional)
# Docs: 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_somatic: string

# vc combine phased variants max vaf delta somatic (Optional)
# Docs: Component SNVs/INDELs of MNV calls are output only if the VAF of the component 
# call is greater than that of the MNV by more than 0.1. The VAF difference 
# threshold for outputting component calls along with MNV calls can be controlled by 
# the --vc-combine-phased-variants-max-vaf-delta option.
# This option is mutually exclusive with --vc-mnv-emit-component-calls
vc_combine_phased_variants_max_vaf_delta_somatic: string

# vc decoy contigs (Optional)
# Docs: The --vc-decoy-contigs option specifies a comma-separated list of contigs to skip during variant calling.
# This option can be set in the configuration file.
vc_decoy_contigs: string

# vc enable af filter (Optional)
# Docs: Enables the allele frequency filter. The default value is false. When set to true, the VCF excludes variants
# with allele frequencies below the AF call threshold or variants with an allele frequency below the AF filter
# threshold and tagged with low AF filter tag. The default AF call threshold is 1% and the default AF filter
# threshold is 5%.
# To change the threshold values, use the following command line options:
#   --vc-af-callthreshold and --vc-af-filter-threshold.
vc_enable_af_filter: false

# vc enable baf (Optional)
# Docs: Enable or disable B-allele frequency output. Enabled by default.
vc_enable_baf: false

# vc enable decoy contigs (Optional)
# Docs: If --vc-enable-decoy-contigs is set to true, variant calls on the decoy contigs are enabled.
# The default value is false.
vc_enable_decoy_contigs: false

# vc enable gatk acceleration (Optional)
# Docs: If is set to true, the variant caller runs in GATK mode
# (concordant with GATK 3.7 in germline mode and GATK 4.0 in somatic mode).
vc_enable_gatk_acceleration: false

# vc enable liquid tumor mode (Optional)
# Docs: In a tumor-normal analysis, DRAGEN accounts for tumor-in-normal (TiN) contamination by running liquid
# tumor mode. Liquid tumor mode is disabled by default. When liquid tumor mode is enabled, DRAGEN is
# able to call variants in the presence of TiN contamination up to a specified maximum tolerance level.
# vc-enable-liquid-tumor-mode enables liquid tumor mode with a default maximum contamination
# TiN tolerance of 0.15. If using the default maximum contamination TiN tolerance, somatic variants are
# expected to be observed in the normal sample with allele frequencies up to 15% of the corresponding
# allele in the tumor sample.
vc_enable_liquid_tumor_mode: false

# vc enable non homoref normal filter (Optional)
# Docs: Enables the non-homref normal filter. The default value is true. When set to true, the VCF filters out
# variants if the normal sample genotype is not a homozygous reference.
vc_enable_non_homref_normal_filter: false

# vc enable non primary allelic filter (Optional)
# Docs: 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: false

# vc enable orientation bias filter (Optional)
# Docs: Enables the orientation bias filter. The default value is false, which means the option is disabled.
vc_enable_orientation_bias_filter: false

# vc enable orientation bias filter artifacts (Optional)
# Docs: The artifact type to be filtered can be specified with the --vc-orientation-bias-filter-artifacts option.
# The default is C/T,G/T, which correspond to OxoG and FFPE artifacts. Valid values include C/T, or G/T, or C/T,G/T,C/A.
# An artifact (or an artifact and its reverse compliment) cannot be listed twice.
# For example, C/T,G/A is not valid, because C->G and T->A are reverse compliments.
vc_enable_orientation_bias_filter_artifacts: string

# vc enable phasing (Optional)
# Docs: The -vc-enable-phasing option enables variants to be phased when possible. The default value is true.
vc_enable_phasing: false

# vc enable roh (Optional)
# Docs: Enable or disable the ROH caller by setting this option to true or false. Enabled by default for human autosomes only.
vc_enable_roh: false

# vc enable triallelic filter (Optional)
# Docs: Enables the multiallelic filter. The default is true.
vc_enable_triallelic_filter: false

# vc enable unequal ntd (Optional)
# Docs: Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
# Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
# In addition, NTD error estimation accounts for non-strand-specific biases such as sample-wide elevation of a certain SNV type,
# eg C->T or any other transition or transversion.
# NTD error estimation can also capture the biases in a trinucleotide context.
vc_enable_unequal_ntd: false

# vc enable vcf output (Optional)
# Docs: The -vc-enable-vcf-output option enables VCF file output during a gVCF run. The default value is false.
vc_enable_vcf_output: false

# vc forcegt vcf (Optional)
# Docs: AGENsupports force genotyping (ForceGT) for Germline SNV variant calling.
# To use ForceGT, use the --vc-forcegt-vcf option with a list of small variants to force genotype.
# The input list of small variants can be a .vcf or .vcf.gz file.

# The current limitations of ForceGT are as follows:
# *	ForceGT is supported for Germline SNV variant calling in the V3 mode.
# The V1, V2, and V2+ modes are not supported.
# *	ForceGT is not supported for Somatic SNV variant calling.
# *	ForceGT variants do not propagate through Joint Genotyping.
vc_forcegt_vcf:
  class: File
  location: icav2://project_id/path/to/file

# vc hard filter (Optional)
# Docs: DRAGEN provides post-VCF variant filtering based on annotations present in the VCF records.
# However, due to the nature of DRAGEN's algorithms, which incorporate the hypothesis of correlated errors
# from within the core of variant caller, the pipeline has improved capabilities in distinguishing
# the true variants from noise, and therefore the dependency on post-VCF filtering is substantially reduced.
# For this reason, the default post-VCF filtering in DRAGEN is very simple
vc_hard_filter: string

# vc hotspot log10 prior boost (Optional)
# Docs: The size of the hotspot adjustment can be controlled via vc-hotspotlog10-prior-boost,
# which has a default value of 4 (log10 scale) corresponding to an increase of 40 phred.
vc_hotspot_log10_prior_boost: string

# vc max reads per active region (Optional)
# Docs: specifies the maximum number of reads covering a given active region.
# Default is 10000 for the somatic workflow
vc_max_reads_per_active_region: string

# vc max reads per raw region (Optional)
# Docs: specifies the maximum number of reads covering a given raw region.
# Default is 30000 for the somatic workflow
vc_max_reads_per_raw_region: string

# vc min tumor read qual (Optional)
# Docs: The --vc-min-tumor-read-qual option specifies the minimum read quality (MAPQ) to be considered for
# variant calling. The default value is 3 for tumor-normal analysis or 20 for tumor-only analysis.
vc_min_tumor_read_qual: string

# vc mnv emit component calls somatic (Optional)
# Docs: To output all component SNVs/INDELs of MNVs, regardless of VAF difference, 
# when enabled, use the option --vc-mnv-emit-component-calls. 
# This option is mutually exclusive with --vc-combine-phased-variants-max-vaf-delta
vc_mnv_emit_component_calls_somatic: false

# vc remove all soft clips (Optional)
# Docs: If is set to true, the variant caller does not use soft clips of reads to determine variants.
vc_remove_all_soft_clips: false

# vc roh blacklist bed (Optional)
# Docs: If provided, the ROH caller ignores variants that are contained in any region in the blacklist BED file.
# DRAGEN distributes blacklist files for all popular human genomes and automatically selects a blacklist to
# match the genome in use, unless this option is used explicitly select a file.
vc_roh_blacklist_bed:
  class: File
  location: icav2://project_id/path/to/file

# vc somatic hotspots (Optional)
# Docs: The somatic hotspots option allows an input VCF to specify the positions where the risk for somatic
# mutations are assumed to be significantly elevated. DRAGEN genotyping priors are boosted for all
# postions specified in the VCF, so it is possible to call a variant at one of these sites with fewer supporting
# reads. The cosmic database in VCF format can be used as one source of prior information to boost
# sensitivity for known somatic mutations.
vc_somatic_hotspots:
  class: File
  location: icav2://project_id/path/to/file

# vc sq call threshold (Optional)
# Docs: Emits calls in the VCF. The default is 3.
# If the value for vc-sq-filter-threshold is lower than vc-sq-callthreshold,
# the filter threshold value is used instead of the call threshold value
vc_sq_call_threshold: string

# vc sq filter threshold (Optional)
# Docs: Marks emitted VCF calls as filtered.
# The default is 17.5 for tumor-normal and 6.5 for tumor-only.
vc_sq_filter_threshold: string

# vc target bed (Optional)
# Docs: This is an optional command line input that restricts processing of the small variant caller,
# target bed related coverage, and callability metrics to regions specified in a BED file.
vc_target_bed:
  class: File
  location: icav2://project_id/path/to/file

# vc target bed padding (Optional)
# Docs: This is an optional command line input that can be used to pad all of the target
# BED regions with the specified value.
# For example, if a BED region is 1:1000-2000 and a padding value of 100 is used,
# it is equivalent to using a BED region of 1:900-2100 and a padding value of 0.

# Any padding added to --vc-target-bed-padding is used by the small variant caller
# and by the target bed coverage/callability reports. The default padding is 0.
vc_target_bed_padding: string

# vc target coverage (Optional)
# Docs: The --vc-target-coverage option specifies the target coverage for down-sampling.
# The default value is 500 for germline mode and 50 for somatic mode.
vc_target_coverage: string

# vc target vaf somatic (Optional)
# Docs: The vc-target-vaf is used to select the variant allele frequencies of interest.
# The variant caller will aim to detect variants with allele frequencies larger than this setting.
# We recommend adding a small safety factor, e.g. to ensure variants in the ballpark of 1% are detected,
# the minimum vc-target-vaf can be specified as 0.009 (0.9%). This setting will not apply a hard threshold,
# and it is possible to detect variants with allele frequencies lower than the selected threshold.
# On high coverage and clean datasets, a lower target-vaf may help increase sensitivity.
# On noisy samples (like FFPE) a higher target-vaf (like 0.03) maybe help reduce false positives.
# Using a low target-vaf may also increase runtime. Set the vc-target-vaf to 0 to disable this feature.
# When this feature is disabled the variant caller will require at least 2 supporting reads to discover a candidate variant.
# Default=0.01.
vc_target_vaf_somatic: string

# vc tin contam tolerance (Optional)
# Docs: vc-tin-contam-tolerance enables liquid tumor mode and allows you to
# set the maximum contamination TiN tolerance. The maximum contamination TiN tolerance must be
# greater than zero. For example, vc-tin-contam-tolerance=-0.1.
vc_tin_contam_tolerance: string

Json

Click to expand!

{
    "bam_input": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "cnv_enable_self_normalization": false,
    "cnv_normal_b_allele_vcf": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "cnv_normal_cnv_vcf": false,
    "cnv_population_b_allele_vcf": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "cnv_somatic_enable_het_calling": false,
    "cnv_somatic_enable_lower_ploidy_limit": false,
    "cnv_somatic_essential_genes_bed": "string",
    "cnv_use_somatic_vc_baf": false,
    "cnv_use_somatic_vc_vaf": false,
    "cram_input": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "cram_reference": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "dbsnp_annotation": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "dedup_min_qual": "string",
    "dedup_min_qual_germline": "string",
    "dedup_min_qual_somatic": "string",
    "enable_cnv": false,
    "enable_duplicate_marking": false,
    "enable_duplicate_marking_germline": false,
    "enable_duplicate_marking_somatic": false,
    "enable_hla": false,
    "enable_hrd": false,
    "enable_map_align": false,
    "enable_map_align_germline": false,
    "enable_map_align_output": false,
    "enable_map_align_output_germline": false,
    "enable_map_align_output_somatic": false,
    "enable_map_align_somatic": false,
    "enable_rna": false,
    "enable_sort": false,
    "enable_sort_germline": false,
    "enable_sort_somatic": false,
    "enable_sv": false,
    "enable_sv_germline": false,
    "enable_sv_somatic": false,
    "enable_tmb": false,
    "fastq_list": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "fastq_list_rows": [
        {
            "rgid": "string",
            "rglb": "string",
            "rgsm": "string",
            "lane": "string",
            "read_1": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            },
            "read_2": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            }
        }
    ],
    "hla_allele_frequency_file": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "hla_bed_file": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "hla_min_reads": "string",
    "hla_reference_file": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "hla_tiebreaker_threshold": "string",
    "hla_zygosity_threshold": "string",
    "lic_instance_id_location": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "output_prefix_germline": "string",
    "output_prefix_somatic": "string",
    "qc_coverage_ignore_overlaps": false,
    "qc_coverage_region_1": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "qc_coverage_region_2": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "qc_coverage_region_3": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "reference_tar": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "repeat_genotype_enable": false,
    "repeat_genotype_specs": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "repeat_genotype_use_catalog": "default",
    "sample_sex": "male",
    "sv_call_regions_bed": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "sv_discovery": false,
    "sv_enable_liquid_tumor_mode": false,
    "sv_enable_somatic_ins_tandup_hotspot_regions": false,
    "sv_exome": false,
    "sv_forcegt_vcf": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "sv_output_contigs": false,
    "sv_region": "string",
    "sv_se_overlap_pair_evidence": false,
    "sv_somatic_ins_tandup_hotspot_regions_bed": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "sv_tin_contam_tolerance": "string",
    "tmb_db_threshold": "string",
    "tmb_vaf_threshold": "string",
    "tumor_bam_input": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "tumor_cram_input": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "tumor_fastq_list": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "tumor_fastq_list_rows": [
        {
            "rgid": "string",
            "rglb": "string",
            "rgsm": "string",
            "lane": "string",
            "read_1": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            },
            "read_2": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            }
        }
    ],
    "vc_af_call_threshold": "string",
    "vc_af_call_threshold_mito": false,
    "vc_af_filter_threshold": "string",
    "vc_af_filter_threshold_mito": "string",
    "vc_base_qual_threshold": "string",
    "vc_base_qual_threshold_germline": "string",
    "vc_base_qual_threshold_somatic": "string",
    "vc_callability_normal_thresh": "string",
    "vc_callability_tumor_thresh": "string",
    "vc_combine_phased_variants_distance_somatic": "string",
    "vc_combine_phased_variants_max_vaf_delta_somatic": "string",
    "vc_decoy_contigs": "string",
    "vc_enable_af_filter": false,
    "vc_enable_baf": false,
    "vc_enable_decoy_contigs": false,
    "vc_enable_gatk_acceleration": false,
    "vc_enable_liquid_tumor_mode": false,
    "vc_enable_non_homref_normal_filter": false,
    "vc_enable_non_primary_allelic_filter": false,
    "vc_enable_orientation_bias_filter": false,
    "vc_enable_orientation_bias_filter_artifacts": "string",
    "vc_enable_phasing": false,
    "vc_enable_roh": false,
    "vc_enable_triallelic_filter": false,
    "vc_enable_unequal_ntd": false,
    "vc_enable_vcf_output": false,
    "vc_forcegt_vcf": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "vc_hard_filter": "string",
    "vc_hotspot_log10_prior_boost": "string",
    "vc_max_reads_per_active_region": "string",
    "vc_max_reads_per_raw_region": "string",
    "vc_min_tumor_read_qual": "string",
    "vc_mnv_emit_component_calls_somatic": false,
    "vc_remove_all_soft_clips": false,
    "vc_roh_blacklist_bed": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "vc_somatic_hotspots": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "vc_sq_call_threshold": "string",
    "vc_sq_filter_threshold": "string",
    "vc_target_bed": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "vc_target_bed_padding": "string",
    "vc_target_coverage": "string",
    "vc_target_vaf_somatic": "string",
    "vc_tin_contam_tolerance": "string"
}

Outputs Template

Click to expand!

{
    "dragen_germline_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "dragen_somatic_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "germline_snv_vcf_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "multiqc_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "normal_bam_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "somatic_snv_vcf_hard_filtered_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "somatic_snv_vcf_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "somatic_structural_vcf_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "tumor_bam_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    }
}

Overrides Template

Zipped workflow

Click to expand!

[
    "workflow.cwl#dragen-somatic-with-germline-pipeline--4.2.4/create_dummy_file_step",
    "workflow.cwl#dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_germline_step",
    "workflow.cwl#dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_qc_step",
    "workflow.cwl#dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_somatic_step"
]

Packed workflow

Click to expand!

[
    "#main/create_dummy_file_step",
    "#main/run_dragen_germline_step",
    "#main/run_dragen_qc_step",
    "#main/run_dragen_somatic_step"
]

Inputs

Click to expand!

bam input

ID: bam_input

Optional: True
Type: File
Docs:
Input a normal BAM file for the variant calling stage

cnv enable self normalization

ID: cnv_enable_self_normalization

Optional: True
Type: boolean
Docs:
Enable CNV self normalization.
Self Normalization requires that the DRAGEN hash table be generated with the enable-cnv=true option.

cnv normal b allele vcf

ID: cnv_normal_b_allele_vcf

Optional: True
Type: File
Docs:
Specify a matched normal SNV VCF.

cnv normal cnv vcf

ID: cnv_normal_cnv_vcf

Optional: True
Type: boolean
Docs:
Specify germline CNVs from the matched normal sample.

cnv population b allele vcf

ID: cnv_population_b_allele_vcf

Optional: True
Type: File
Docs:
Specify a population SNP catalog.

cnv somatic enable het calling

ID: cnv_somatic_enable_het_calling

Optional: True
Type: boolean
Docs:
Enable HET-calling mode for heterogeneous segments.

cnv somatic enable lower ploidy limit

ID: cnv_somatic_enable_lower_ploidy_limit

Optional: True
Type: boolean
Docs:
To improve accuracy on the tumor ploidy model estimation, the somatic WGS CNV caller estimates whether the chosen model calls
homozygous deletions on regions that are likely to reduce the overall fitness of cells,
which are therefore deemed to be "essential" and under negative selection.
In the current literature, recent efforts tried to map such cell-essential genes (eg, in 2015 - https://www.science.org/doi/10.1126/science.aac7041).
The check on essential regions is controlled with --cnv-somatic-enable-lower-ploidy-limit (default true).

cnv somatic essential genes bed

ID: cnv_somatic_essential_genes_bed

Optional: True
Type: ['string', 'File']
Docs:
Default bedfiles describing the essential regions are provided for hg19, GRCh37, hs37d5, GRCh38,
but a custom bedfile can also be provided in input through the
--cnv-somatic-essential-genes-bed=<BEDFILE_PATH> parameter.
In such case, the feature is automatically enabled.
A custom essential regions bedfile needs to have the following format: 4-column, tab-separated,
where the first 3 columns identify the coordinates of the essential region (chromosome, 0-based start, excluded end).
The fourth column is the region id (string type). For the purpose of the algorithm, currently only the first 3 columns are used.
However, the fourth might be helpful to investigate manually which regions drove the decisions on model plausibility made by the caller.

cnv use somatic vc baf

ID: cnv_use_somatic_vc_baf

Optional: True
Type: boolean
Docs:
If running in tumor-normal mode with the SNV caller enabled, use this option
to specify the germline heterozygous sites.

cnv use somatic vc vaf

ID: cnv_use_somatic_vc_vaf

Optional: True
Type: boolean
Docs:
Use the variant allele frequencies (VAFs) from the somatic SNVs to help select
the tumor model for the sample.

cram input

ID: cram_input

Optional: True
Type: File
Docs:
Input a normal CRAM file for the variant calling stage

cram reference

ID: cram_reference

Optional: True
Type: File
Docs:
Path to the reference fasta file for the CRAM input.
Required only if the input is a cram file AND not the reference in the tarball

dbsnp annotation

ID: dbsnp_annotation

Optional: True
Type: File
Docs:
In Germline, Tumor-Normal somatic, or Tumor-Only somatic modes,
DRAGEN can look up variant calls in a dbSNP database and add annotations for any matches that it finds there.
To enable the dbSNP database search, set the --dbsnp option to the full path to the dbSNP database
VCF or .vcf.gz file, which must be sorted in reference order.

deduplicate minimum quality

ID: dedup_min_qual

Optional: True
Type: int
Docs:
Specifies the Phred quality score below which a base should be excluded from the quality score
calculation used for choosing among duplicate reads.

deduplicate minimum quality germline

ID: dedup_min_qual_germline

Optional: True
Type: int
Docs:
Specifies the Phred quality score below which a base should be excluded from the quality score
calculation used for choosing among duplicate reads.

deduplicate minimum quality somatic

ID: dedup_min_qual_somatic

Optional: True
Type: int
Docs:
Specifies the Phred quality score below which a base should be excluded from the quality score
calculation used for choosing among duplicate reads.

enable cnv calling

ID: enable_cnv

Optional: True
Type: boolean
Docs:
Enable CNV processing in the DRAGEN Host Software.

enable duplicate marking

ID: enable_duplicate_marking

Optional: True
Type: boolean
Docs:
Enable the flagging of duplicate output
alignment records.

enable duplicate marking germline

ID: enable_duplicate_marking_germline

Optional: True
Type: boolean
Docs:
Enable the flagging of duplicate output
alignment records.

enable duplicate marking somatic

ID: enable_duplicate_marking_somatic

Optional: True
Type: boolean
Docs:
Enable the flagging of duplicate output
alignment records.

enable hla

ID: enable_hla

Optional: True
Type: boolean
Docs:
Enable HLA typing by setting --enable-hla flag to true

enable hrd

ID: enable_hrd

Optional: True
Type: boolean
Docs:
Set to true to enable HRD scoring to quantify genomic instability.
Requires somatic CNV calls.

enable map align

ID: enable_map_align

Optional: True
Type: boolean
Docs:
Enabled by default since --enable-variant-caller option is set to true.
Set this value to false if using bam_input

enable map align germline

ID: enable_map_align_germline

Optional: True
Type: boolean
Docs:
Enabled by default since --enable-variant-caller option is set to true.
Set this value to false if using bam_input

enable map align output

ID: enable_map_align_output

Optional: True
Type: boolean
Docs:
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 germline

ID: enable_map_align_output_germline

Optional: True
Type: boolean
Docs:
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 somatic

ID: enable_map_align_output_somatic

Optional: True
Type: boolean
Docs:
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 somatic

ID: enable_map_align_somatic

Optional: True
Type: boolean
Docs:
Enabled by default since --enable-variant-caller option is set to true.
Set this value to false if using bam_input

enable rna

ID: enable_rna

Optional: True
Type: boolean
Docs:
Set this option for running RNA samples through T/N workflow

enable sort

ID: enable_sort

Optional: True
Type: boolean
Docs:
True by default, only set this to false if using --bam-input parameter

enable sort germline

ID: enable_sort_germline

Optional: True
Type: boolean
Docs:
True by default, only set this to false if using --bam-input parameter

enable sort somatic

ID: enable_sort_somatic

Optional: True
Type: boolean
Docs:
True by default, only set this to false if using --bam-input parameter

enable sv

ID: enable_sv

Optional: True
Type: boolean
Docs:
Enable/disable structural variant
caller. Default is false.

enable sv germline

ID: enable_sv_germline

Optional: True
Type: boolean
Docs:
Enable/disable structural variant
caller. Default is false.

enable sv somatic

ID: enable_sv_somatic

Optional: True
Type: boolean
Docs:
Enable/disable structural variant
caller. Default is false.

enable tmb

ID: enable_tmb

Optional: True
Type: boolean
Docs:
Enables TMB. If set, the small variant caller, Illumina Annotation Engine,
and the related callability report are enabled.

fastq list

ID: fastq_list

Optional: True
Type: File
Docs:
CSV file that contains a list of FASTQ files for normal sample
to process.

Row of fastq lists

ID: fastq_list_rows

Optional: True
Type: fastq-list-row[]
Docs:
The row of fastq lists.
Each row has the following attributes:

• RGID
• RGLB
• RGSM
• Lane
• Read1File
• Read2File (optional)

hla allele frequency file

ID: hla_allele_frequency_file

Optional: True
Type: File
Docs:
Use the population-level HLA allele frequency file to break ties if one or more HLA allele produces the same or similar results.
The input HLA allele frequency file must be in CSV format and contain the HLA alleles and the occurrence frequency in population.
If --hla-allele-frequency-file is not specified, DRAGEN automatically uses hla_classI_allele_frequency.csv from /opt/edico/config/.
Population-level allele frequencies can be obtained from the Allele Frequency Net database.

hla bed file

ID: hla_bed_file

Optional: True
Type: File
Docs:
Use the HLA region BED input file to specify the region to extract HLA reads from.
DRAGEN HLA Caller parses the input file for regions within the BED file, and then
extracts reads accordingly to align with the HLA allele reference.

hla min reads

ID: hla_min_reads

Optional: True
Type: int
Docs:
Set the minimum number of reads to align to HLA alleles to ensure sufficient coverage and perform HLA typing.
The default value is 1000 and suggested for WES samples. If using samples with less coverage, you can use a
lower threshold value.

hla reference file

ID: hla_reference_file

Optional: True
Type: File
Docs:
Use the HLA allele reference file to specify the reference alleles to align against.
The input HLA reference file must be in FASTA format and contain the protein sequence separated into exons.
If --hla-reference-file is not specified, DRAGEN uses hla_classI_ref_freq.fasta from /opt/edico/config/.
The reference HLA sequences are obtained from the IMGT/HLA database.

hla tiebreaker threshold

ID: hla_tiebreaker_threshold

Optional: True
Type: float
Docs:
If more than one allele has a similar number of reads aligned and there is not a clear indicator for the best allele,
the alleles are considered as ties. The HLA Caller places the tied alleles into a candidate set for tie breaking based
on the population allele frequency. If an allele has more than the specified fraction of reads aligned (normalized to
the top hit), then the allele is included into the candidate set for tie breaking. The default value is 0.97.

hla zygosity threshold

ID: hla_zygosity_threshold

Optional: True
Type: float
Docs:
If the minor allele at a given locus has fewer reads mapped than a fraction of the read count of the major allele,
then the HLA Caller infers homozygosity for the given HLA-I gene. You can use this option to specify the fraction value.
The default value is 0.15.

license instance id location

ID: lic_instance_id_location

Optional: True
Type: ['File', 'string']
Docs:
You may wish to place your own in.
Optional value, default set to /opt/instance-identity
which is a path inside the dragen container

output prefix germline

ID: output_prefix_germline

Optional: False
Type: string
Docs:
The prefix given to all outputs for the dragen germline pipeline

output prefix somatic

ID: output_prefix_somatic

Optional: False
Type: string
Docs:
The prefix given to all outputs for the dragen somatic pipeline

qc coverage ignore overlaps

ID: qc_coverage_ignore_overlaps

Optional: True
Type: boolean
Docs:
Set to true to resolve all of the alignments for each fragment and avoid double-counting any
overlapping bases. This might result in marginally longer run times.
This option also requires setting --enable-map-align=true.

qc coverage region 1

ID: qc_coverage_region_1

Optional: True
Type: File
Docs:
Generates coverage region report using bed file 1.

qc coverage region 2

ID: qc_coverage_region_2

Optional: True
Type: File
Docs:
Generates coverage region report using bed file 2.

qc coverage region 3

ID: qc_coverage_region_3

Optional: True
Type: File
Docs:
Generates coverage region report using bed file 3.

reference tar

ID: reference_tar

Optional: False
Type: File
Docs:
Path to ref data tarball

repeat genotype enable

ID: repeat_genotype_enable

Optional: True
Type: boolean
Docs:
Enables repeat expansion detection.

repeat genotype specs

ID: repeat_genotype_specs

Optional: True
Type: File
Docs:
Specifies the full path to the JSON file that contains the
repeat variant catalog (specification) describing the loci to call.
If the option is not provided, DRAGEN attempts to autodetect the applicable catalog file
from /opt/edico/repeat-specs/ based on the reference provided.

repeat genotype use catalog

ID: repeat_genotype_use_catalog

Optional: True
Type: [ default | default_plus_smn | expanded ]
Docs:
Repeat variant catalog type to use (default - ~60 repeats, default_plus_smn -
same as default with SMN repeat, expanded - ~50K repeats)

sample sex

ID: sample_sex

Optional: True
Type: [ male | female ]
Docs:
Specifies the sex of a sample

sv call regions bed

ID: sv_call_regions_bed

Optional: True
Type: File
Docs:
Specifies a BED file containing the set of regions to call.

sv discovery

ID: sv_discovery

Optional: True
Type: boolean
Docs:
Enable SV discovery. This flag can be set to false only when --sv-forcegt-vcf is used.
When set to false, SV discovery is disabled and only the forced genotyping input variants
are processed. The default is true.

sv enable liquid tumor mode

ID: sv_enable_liquid_tumor_mode

Optional: True
Type: boolean
Docs:
Enable liquid tumor mode.

sv enable somatic ins tandup hotspot regions

ID: sv_enable_somatic_ins_tandup_hotspot_regions

Optional: True
Type: boolean
Docs:
Enable or disable the ITD hotspot region input. The default is true in somatic variant analysis.

sv exome

ID: sv_exome

Optional: True
Type: boolean
Docs:
Set to true to configure the variant caller for targeted sequencing inputs,
which includes disabling high depth filters.
In integrated mode, the default is to autodetect targeted sequencing input,
and in standalone mode the default is false.

sv forcegt vcf

ID: sv_forcegt_vcf

Optional: True
Type: File
Docs:
Specify a VCF of structural variants for forced genotyping. The variants are scored and emitted
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 output contigs

ID: sv_output_contigs

Optional: True
Type: boolean
Docs:
Set to true to have assembled contig sequences output in a VCF file. The default is false.

sv region

ID: sv_region

Optional: True
Type: string
Docs:
Limit the analysis to a specified region of the genome for debugging purposes.
This option can be specified multiple times to build a list of regions.
The value must be in the format "chr:startPos-endPos"..

sv use overlap pair evidence

ID: sv_se_overlap_pair_evidence

Optional: True
Type: boolean
Docs:
Allow overlapping read pairs to be considered as evidence.
By default, DRAGEN uses autodetect on the fraction of overlapping read pairs if <20%.

sv somatic ins tandup hotspot regions bed

ID: sv_somatic_ins_tandup_hotspot_regions_bed

Optional: True
Type: File
Docs:
Specify a BED of ITD hotspot regions to increase sensitivity for calling ITDs in somatic variant analysis.
By default, DRAGEN SV automatically selects areference-specific hotspots BED file from
/opt/edico/config/sv_somatic_ins_tandup_hotspot_*.bed.

sv tin contam tolerance

ID: sv_tin_contam_tolerance

Optional: True
Type: float
Docs:
Set the Tumor-in-Normal (TiN) contamination tolerance level.
You can enter any value between 0-1. The default maximum TiN contamination tolerance is 0.15.

tmb db threshold

ID: tmb_db_threshold

Optional: True
Type: int
Docs:
Specify the minimum allele count (total number of observations) for an allele in gnomAD or 1000 Genome
to be considered a germline variant. Variant calls that have the same positions and allele are ignored
from the TMB calculation. The default value is 10.

tmb vaf threshold

ID: tmb_vaf_threshold

Optional: True
Type: float
Docs:
Specify the minimum VAF threshold for a variant. Variants that do not meet the threshold are filtered out.
The default value is 0.05.

tumor bam input

ID: tumor_bam_input

Optional: True
Type: File
Docs:
Input a tumor BAM file for the variant calling stage

tumor cram input

ID: tumor_cram_input

Optional: True
Type: File
Docs:
Input a tumor CRAM file for the variant calling stage

tumor fastq list

ID: tumor_fastq_list

Optional: True
Type: File
Docs:
CSV file that contains a list of FASTQ files
to process.

Row of fastq lists

ID: tumor_fastq_list_rows

Optional: True
Type: fastq-list-row[]
Docs:
The row of fastq lists.
Each row has the following attributes:

• RGID
• RGLB
• RGSM
• Lane
• Read1File
• Read2File (optional)

vc af call threshold

ID: vc_af_call_threshold

Optional: True
Type: float
Docs:
Set the allele frequency call threshold to emit a call in the VCF if the AF filter is enabled.
The default is 0.01.

vc af call threshold mito

ID: vc_af_call_threshold_mito

Optional: True
Type: boolean
Docs:
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 filter threshold

ID: vc_af_filter_threshold

Optional: True
Type: float
Docs:
Set the allele frequency filter threshold to mark emitted VCF calls as filtered if the AF filter is
enabled.
The default is 0.05.

vc af filter threshold mito

ID: vc_af_filter_threshold_mito

Optional: True
Type: float
Docs:
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 base qual threshold

ID: vc_base_qual_threshold

Optional: True
Type: int
Docs:
(Replaces --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 base qual threshold germline

ID: vc_base_qual_threshold_germline

Optional: True
Type: int
Docs:
(Replaces --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 base qual threshold somatic

ID: vc_base_qual_threshold_somatic

Optional: True
Type: int
Docs:
(Replaces --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 callability normal thresh

ID: vc_callability_normal_thresh

Optional: True
Type: int
Docs:
The --vc-callability-normal-thresh option specifies the callability threshold for normal samples.
The somatic callable regions report includes all regions with normal coverage above the normal threshold.

vc callability tumor thresh

ID: vc_callability_tumor_thresh

Optional: True
Type: int
Docs:
The --vc-callability-tumor-thresh option specifies the callability threshold for tumor samples. The
somatic callable regions report includes all regions with tumor coverage above the tumor threshold.

vc combine phased variants distance somatic

ID: vc_combine_phased_variants_distance_somatic

Optional: True
Type: int
Docs:
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 max vaf delta somatic

ID: vc_combine_phased_variants_max_vaf_delta_somatic

Optional: True
Type: float
Docs:
Component SNVs/INDELs of MNV calls are output only if the VAF of the component
call is greater than that of the MNV by more than 0.1. The VAF difference
threshold for outputting component calls along with MNV calls can be controlled by
the --vc-combine-phased-variants-max-vaf-delta option.
This option is mutually exclusive with --vc-mnv-emit-component-calls

vc decoy contigs

ID: vc_decoy_contigs

Optional: True
Type: string
Docs:
The --vc-decoy-contigs option specifies a comma-separated list of contigs to skip during variant calling.
This option can be set in the configuration file.

vc enable af filter

ID: vc_enable_af_filter

Optional: True
Type: boolean
Docs:
Enables the allele frequency filter. The default value is false. When set to true, the VCF excludes variants
with allele frequencies below the AF call threshold or variants with an allele frequency below the AF filter
threshold and tagged with low AF filter tag. The default AF call threshold is 1% and the default AF filter
threshold is 5%.
To change the threshold values, use the following command line options:
--vc-af-callthreshold and --vc-af-filter-threshold.

vc enable baf

ID: vc_enable_baf

Optional: True
Type: boolean
Docs:
Enable or disable B-allele frequency output. Enabled by default.

vc enable decoy contigs

ID: vc_enable_decoy_contigs

Optional: True
Type: boolean
Docs:
If --vc-enable-decoy-contigs is set to true, variant calls on the decoy contigs are enabled.
The default value is false.

vc enable gatk acceleration

ID: vc_enable_gatk_acceleration

Optional: True
Type: boolean
Docs:
If is set to true, the variant caller runs in GATK mode
(concordant with GATK 3.7 in germline mode and GATK 4.0 in somatic mode).

vc enable liquid tumor mode

ID: vc_enable_liquid_tumor_mode

Optional: True
Type: boolean
Docs:
In a tumor-normal analysis, DRAGEN accounts for tumor-in-normal (TiN) contamination by running liquid
tumor mode. Liquid tumor mode is disabled by default. When liquid tumor mode is enabled, DRAGEN is
able to call variants in the presence of TiN contamination up to a specified maximum tolerance level.
vc-enable-liquid-tumor-mode enables liquid tumor mode with a default maximum contamination
TiN tolerance of 0.15. If using the default maximum contamination TiN tolerance, somatic variants are
expected to be observed in the normal sample with allele frequencies up to 15% of the corresponding
allele in the tumor sample.

vc enable non homoref normal filter

ID: vc_enable_non_homref_normal_filter

Optional: True
Type: boolean
Docs:
Enables the non-homref normal filter. The default value is true. When set to true, the VCF filters out
variants if the normal sample genotype is not a homozygous reference.

vc enable non primary allelic filter

ID: vc_enable_non_primary_allelic_filter

Optional: True
Type: boolean
Docs:
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 orientation bias filter

ID: vc_enable_orientation_bias_filter

Optional: True
Type: boolean
Docs:
Enables the orientation bias filter. The default value is false, which means the option is disabled.

vc enable orientation bias filter artifacts

ID: vc_enable_orientation_bias_filter_artifacts

Optional: True
Type: string
Docs:
The artifact type to be filtered can be specified with the --vc-orientation-bias-filter-artifacts option.
The default is C/T,G/T, which correspond to OxoG and FFPE artifacts. Valid values include C/T, or G/T, or C/T,G/T,C/A.
An artifact (or an artifact and its reverse compliment) cannot be listed twice.
For example, C/T,G/A is not valid, because C->G and T->A are reverse compliments.

vc enable phasing

ID: vc_enable_phasing

Optional: True
Type: boolean
Docs:
The -vc-enable-phasing option enables variants to be phased when possible. The default value is true.

vc enable roh

ID: vc_enable_roh

Optional: True
Type: boolean
Docs:
Enable or disable the ROH caller by setting this option to true or false. Enabled by default for human autosomes only.

vc enable triallelic filter

ID: vc_enable_triallelic_filter

Optional: True
Type: boolean
Docs:
Enables the multiallelic filter. The default is true.

vc enable unequal ntd

ID: vc_enable_unequal_ntd

Optional: True
Type: ['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f7766c89220>]
Docs:
Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
In addition, NTD error estimation accounts for non-strand-specific biases such as sample-wide elevation of a certain SNV type,
eg C->T or any other transition or transversion.
NTD error estimation can also capture the biases in a trinucleotide context.

vc enable vcf output

ID: vc_enable_vcf_output

Optional: True
Type: boolean
Docs:
The -vc-enable-vcf-output option enables VCF file output during a gVCF run. The default value is false.

vc forcegt vcf

ID: vc_forcegt_vcf

Optional: True
Type: File
Docs:
AGENsupports force genotyping (ForceGT) for Germline SNV variant calling.
To use ForceGT, use the --vc-forcegt-vcf option with a list of small variants to force genotype.
The input list of small variants can be a .vcf or .vcf.gz file.

The current limitations of ForceGT are as follows:

• ForceGT is supported for Germline SNV variant calling in the V3 mode.
  The V1, V2, and V2+ modes are not supported.
• ForceGT is not supported for Somatic SNV variant calling.
• ForceGT variants do not propagate through Joint Genotyping.

vc hard filter

ID: vc_hard_filter

Optional: True
Type: string
Docs:
DRAGEN provides post-VCF variant filtering based on annotations present in the VCF records.
However, due to the nature of DRAGEN's algorithms, which incorporate the hypothesis of correlated errors
from within the core of variant caller, the pipeline has improved capabilities in distinguishing
the true variants from noise, and therefore the dependency on post-VCF filtering is substantially reduced.
For this reason, the default post-VCF filtering in DRAGEN is very simple

vc hotspot log10 prior boost

ID: vc_hotspot_log10_prior_boost

Optional: True
Type: int
Docs:
The size of the hotspot adjustment can be controlled via vc-hotspotlog10-prior-boost,
which has a default value of 4 (log10 scale) corresponding to an increase of 40 phred.

vc max reads per active region

ID: vc_max_reads_per_active_region

Optional: True
Type: int
Docs:
specifies the maximum number of reads covering a given active region.
Default is 10000 for the somatic workflow

vc max reads per raw region

ID: vc_max_reads_per_raw_region

Optional: True
Type: int
Docs:
specifies the maximum number of reads covering a given raw region.
Default is 30000 for the somatic workflow

vc min tumor read qual

ID: vc_min_tumor_read_qual

Optional: True
Type: int
Docs:
The --vc-min-tumor-read-qual option specifies the minimum read quality (MAPQ) to be considered for
variant calling. The default value is 3 for tumor-normal analysis or 20 for tumor-only analysis.

vc mnv emit component calls somatic

ID: vc_mnv_emit_component_calls_somatic

Optional: True
Type: boolean
Docs:
To output all component SNVs/INDELs of MNVs, regardless of VAF difference,
when enabled, use the option --vc-mnv-emit-component-calls.
This option is mutually exclusive with --vc-combine-phased-variants-max-vaf-delta

vc remove all soft clips

ID: vc_remove_all_soft_clips

Optional: True
Type: boolean
Docs:
If is set to true, the variant caller does not use soft clips of reads to determine variants.

vc roh blacklist bed

ID: vc_roh_blacklist_bed

Optional: True
Type: File
Docs:
If provided, the ROH caller ignores variants that are contained in any region in the blacklist BED file.
DRAGEN distributes blacklist files for all popular human genomes and automatically selects a blacklist to
match the genome in use, unless this option is used explicitly select a file.

vc somatic hotspots

ID: vc_somatic_hotspots

Optional: True
Type: File
Docs:
The somatic hotspots option allows an input VCF to specify the positions where the risk for somatic
mutations are assumed to be significantly elevated. DRAGEN genotyping priors are boosted for all
postions specified in the VCF, so it is possible to call a variant at one of these sites with fewer supporting
reads. The cosmic database in VCF format can be used as one source of prior information to boost
sensitivity for known somatic mutations.

vc sq call threshold

ID: vc_sq_call_threshold

Optional: True
Type: float
Docs:
Emits calls in the VCF. The default is 3.
If the value for vc-sq-filter-threshold is lower than vc-sq-callthreshold,
the filter threshold value is used instead of the call threshold value

vc sq filter threshold

ID: vc_sq_filter_threshold

Optional: True
Type: float
Docs:
Marks emitted VCF calls as filtered.
The default is 17.5 for tumor-normal and 6.5 for tumor-only.

vc target bed

ID: vc_target_bed

Optional: True
Type: File
Docs:
This is an optional command line input that restricts processing of the small variant caller,
target bed related coverage, and callability metrics to regions specified in a BED file.

vc target bed padding

ID: vc_target_bed_padding

Optional: True
Type: int
Docs:
This is an optional command line input that can be used to pad all of the target
BED regions with the specified value.
For example, if a BED region is 1:1000-2000 and a padding value of 100 is used,
it is equivalent to using a BED region of 1:900-2100 and a padding value of 0.

Any padding added to --vc-target-bed-padding is used by the small variant caller
and by the target bed coverage/callability reports. The default padding is 0.

vc target coverage

ID: vc_target_coverage

Optional: True
Type: int
Docs:
The --vc-target-coverage option specifies the target coverage for down-sampling.
The default value is 500 for germline mode and 50 for somatic mode.

vc target vaf somatic

ID: vc_target_vaf_somatic

Optional: True
Type: float
Docs:
The vc-target-vaf is used to select the variant allele frequencies of interest.
The variant caller will aim to detect variants with allele frequencies larger than this setting.
We recommend adding a small safety factor, e.g. to ensure variants in the ballpark of 1% are detected,
the minimum vc-target-vaf can be specified as 0.009 (0.9%). This setting will not apply a hard threshold,
and it is possible to detect variants with allele frequencies lower than the selected threshold.
On high coverage and clean datasets, a lower target-vaf may help increase sensitivity.
On noisy samples (like FFPE) a higher target-vaf (like 0.03) maybe help reduce false positives.
Using a low target-vaf may also increase runtime. Set the vc-target-vaf to 0 to disable this feature.
When this feature is disabled the variant caller will require at least 2 supporting reads to discover a candidate variant.
Default=0.01.

vc tin contam tolerance

ID: vc_tin_contam_tolerance

Optional: True
Type: float
Docs:
vc-tin-contam-tolerance enables liquid tumor mode and allows you to
set the maximum contamination TiN tolerance. The maximum contamination TiN tolerance must be
greater than zero. For example, vc-tin-contam-tolerance=-0.1.

Steps

Click to expand!

Create dummy file

ID: dragen-somatic-with-germline-pipeline--4.2.4/create_dummy_file_step

Step Type: tool
Docs:

Intermediate step for letting multiqc-interop be placed in stream mode

get normal bam out

ID: dragen-somatic-with-germline-pipeline--4.2.4/get_normal_bam_out

Step Type: expression
Docs:

Get the normal bam value from one of the two available options
From the germline step (preferred)
From the somatic step (backup option)

run dragen germline step

ID: dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_germline_step

Step Type: tool
Docs:

Runs the dragen germline workflow on the FPGA.
Takes in either a fastq list as a file or a fastq_list_rows schema object

dragen qc step

ID: dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_qc_step

Step Type: tool
Docs:

The dragen qc step - this takes in an array of dirs

run dragen somatic step

ID: dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_somatic_step

Step Type: tool
Docs:

Run dragen somatic v4.2.4

Outputs

Click to expand!

dragen germline output directory

ID: dragen-somatic-with-germline-pipeline--4.2.4/dragen_germline_output_directory

Optional: False
Output Type: Directory
Docs:
The output directory containing all germline output files

dragen somatic output directory

ID: dragen-somatic-with-germline-pipeline--4.2.4/dragen_somatic_output_directory

Optional: False
Output Type: Directory
Docs:
Output directory containing all outputs of the somatic dragen run

germline snv vcf out

ID: dragen-somatic-with-germline-pipeline--4.2.4/germline_snv_vcf_out

Optional: True
Output Type: File
Docs:
The output vcf file of germline step

multiqc output directory

ID: dragen-somatic-with-germline-pipeline--4.2.4/multiqc_output_directory

Optional: False
Output Type: Directory
Docs:
The output directory for multiqc

output normal bam

ID: dragen-somatic-with-germline-pipeline--4.2.4/normal_bam_out

Optional: True
Output Type: File
Docs:
Bam file of the normal sample

somatic snv vcf filetered

ID: dragen-somatic-with-germline-pipeline--4.2.4/somatic_snv_vcf_hard_filtered_out

Optional: True
Output Type: File
Docs:
Output of the snv vcf filtered tumor calls

somatic snv vcf

ID: dragen-somatic-with-germline-pipeline--4.2.4/somatic_snv_vcf_out

Optional: True
Output Type: File
Docs:
Output of the snv vcf tumor calls

somatic sv vcf filetered

ID: dragen-somatic-with-germline-pipeline--4.2.4/somatic_structural_vcf_out

Optional: True
Output Type: File
Docs:
Output of the sv vcf filtered tumor calls.
Exists only if --enable-sv is set to true.

output tumor bam

ID: dragen-somatic-with-germline-pipeline--4.2.4/tumor_bam_out

Optional: True
Output Type: File
Docs:
Bam file of the tumor sample