Variant Caller Options

dn-cnv-vcf

Joint structural variant VCF from the CNV calling step. If omitted, checks with overlapping copy number variants are skipped.

--dn-cnv-vcf

dn-input-vcf

Joint small variant VCF de novo calling step to be filtered

--dn-input-vcf

dn-output-vcf

File location to which the filtered VCF should be written. If not specified, the input VCF is overwritten.

--dn-output-vcf

dn-sv-vcf

Joint structural variant VCF from the SV calling step. If omitted, checks with overlapping structural variants are skipped.

--dn-sv-vcf

enable-combinegvcfs

Enable/disable combine gVCF run.

--enable-combinegvcfs

enable-joint-genotyping

To enable combine gVCF run, set to true.

--enable-joint-genotyping

enable-multi-sample-gvcf

Enable/disable generation of a multisample gVCF file. If set to true, requires a combined gVCF file as input.

--enable-multi-sample-gvcf

enable-sv

Enable/disable structural variant caller. Default is false.

--enable-sv

enable-vlrd

Enable/disable Virtual Long Read Detection.

--enable-vlrd

panel-of-normals

The path to the panel of normals VCF file.

--panel-of-normals

pedigree-file

Specific to joint calling. The path to a PED pedigree file containing a structured description of the familial relationships between samples. The pedigree file can contain trios. Only pedigree files that contain trios are supported.

--pedigree-file

qc-snp-DeNovo-quality-threshold

The threshold for counting and reporting De Novo SNP variants.

--qc-snp-DeNovo-quality-threshold

qc-indel-DeNovo-quality-threshold

The threshold for counting and reporting De Novo INDEL variants.

--qc-indel-DeNovo-quality-threshold

variant

The path to a single gVCF file. Multiple --variant options can be used on the command line, one

for each gVCF. Up to 500 gVCFs are supported.

--variant

variant-list

The path to a file containing a list of input gVCF files, one file per line, that need to be combined.

--variant-list

vc-af-call-threshold

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

vc-af-filter-threshold

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

vc-callability-normal-threshold

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

--vc-callability-normal-thresh

vc-callability-tumor-threshold

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

--vc-callability-tumor-thresh

vc-decoy-contigs

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

--vc-decoy-contigs

vc-detect-systematic-noise

Sensitive VCF run mode used when building a systematic noise file.

--vc-detect-systematic-noise

vc-emit-ref-confidence

To enable base pair gVCF generation, set to BP_RESOLUTION. To enable banded gVCF generation, set to GVCF.

--vc-emit-ref-confidence

vc-enable-af-filter

Enable/disable the allele frequency filter for somatic mode. Default is false.

--vc-enable-af-filter

vc-enable-baf

Enable or disable B-allele frequency output. The default is true (enabled).

--vc-enable-baf

vc-enable-decoy-contigs

Enable/disable variant calls on decoy contigs. Default is false.

--vc-enable-decoy-contigs

vc-enable-gatk-acceleration

Enable/disable running variant caller in GATK mode.

--vc-enable-gatk-acceleration

vc-enable-liquid-tumor-mode

Enable/disable liquid tumor mode, which takes account of tumor-in-normal contamination. Default is false (disabled).

--vc-enable-liquid-tumor-mode

vc-enable-non-homref-normal-filter

Enable/disable the non-homref normal filter for filtering out somatic variants if the normal sample genotype is not homozygous reference. Default is true (enabled).

--vc-enable-non-homref-normal-filter

vc-enable-orientation-bias-filter

Enable/disable the orientation bias filter.

--vc-enable-orientation-bias-filter

vc-enable-phasing

Enable variants to be phased when possible. Default is true.

--vc-enable-phasing

vc-enable-roh

Enable or disable ROH caller and output. Default is true (enabled).

--vc-enable-roh

vc-enable-triallelic-filter

Enable/disable the multi-allelic filter for somatic mode. Default is true.

--vc-enable-triallelic-filter

vc-enable-vcf-output

Enables VCF file output during a gVCF run. Default is false.

--vc-enable-vcf-output

vc-forcegt-vcf

Force genotyping for Germline small variant calling. A .vcf or .vcf.gz file containing a list of small variants is required.

--vc-forcegt-vcf

vc-gvcf-gq-bands

Define GQ bands for gVCF output. Default is 10 20 30 40 60 80.

--vc-gvcf-gq-bands

vc-hard-filter

Boolean expression for filtering variant calls. Default expression is:

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

vc-max-reads-per-active-region

Maximum number of reads per active region for downsampling. Default is 10000.

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

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

Maximum number of reads covering a given active region for mitochondrial small variant calling. The default is 40000.

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

vc-max-reads-per-raw-region

Maximum number of reads per raw region for downsampling; default is 30000.

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

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

Maximum number of reads covering a specified raw region for mitochondrial small variant calling. The default is 40000.

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

vc-min-base-qual

Minimum base quality to be considered for variant calling. Default is 10.

--vc-min-base-qual

vc-min-call-qual

Minimum variant call quality for emitting a call. Default is 3.

--vc-min-call-qual

vc-min-read-qual

Minimum read quality (MAPQ) to be considered for small variant calling. Default is 1 for germline, 3 for somatic T/N, and 20 for somatic T-only.

--vc-min-read-qual

vc-min-reads-per-start-pos

Minimum number of reads per start position for downsampling. Default is 10.

--vc-min-reads-per-start-pos

vc-min-tumor-read-qual

Minimum tumor read quality (MAPQ) to be considered for variant calling.

vc-orientation-bias-filter-artifacts

Artifact type to be filtered. An artifact (or an artifact and its reverse compliment) cannot be listed twice.

--vc-orientation-bias-filter-artifacts

vc-remove-all-soft-clips

If set to true, variant caller does not use soft clips of reads to determine variants. Default is false.

--vc-remove-all-soft-clips

vc-roh-blacklist-bed

Blacklist BED file for ROH.

--vc-roh-blacklist-bed

vc-sq-call-threshold

Set the SQ call threshold to emit a call in the VCF. The default is 3 for both tumor-normal and tumor-only.

--vc-sq-call-threshold

vc-sq-filter-threshold

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

--vc-sq-filter-threshold

vc-systematic-noise

BED file with site-specific systematic noise level to calculate AQ score (systematic noise score).

--vc-systematic-noise

vc-systematic-noise-filter-threshold

AQ threshold for applying the systematic-noise filter. Default 10 for tumor-normal and 60 for tumor-only.

--vc-systematic-noise-filter-threshold

vc-target-bed

Target regions BED file.

--vc-target-bed

vc-target-bed-padding

Can be used to pad all of the target BED regions with the specified value (optional). If specified, is used by the small variant caller.

--vc-target-bed-padding

vc-target-coverage

Target coverage for downsampling. Default value is 500 for germline and 50 for somatic mode.

--vc-target-coverage

vc-target-coverage-mito

Maximum number of reads with a start position overlapping any given position for mitochondrial small variant calling. Default value is 40000.

--vc-target-coverage-mito