Variant Caller Options

Set --enable-variant-caller to true to enable the variant caller stage for the DRAGEN pipeline.

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. The BED file is a text file containing at least three tab-delimited columns. The first three columns are chromosome, start position, and end position, respectively. The positions are zero-based. For example:

For example:

# header information
chr11 0 246920
chr11 255660 255661

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.

The --vc-sample-name option is deprecated. In end-to-end germline mode (with FASTQ input), the variant caller uses the RGSM value as the sample name. In end-to-end somatic mode, --RGSM-tumor can be used to specify the sample name of the tumor sample. In stand-alone mode (with BAM input), the variant caller uses the RGSM value from the BAM header as the sample name. In somatic mode, the RGSM value from a tumor BAM is as the tumor sample name.

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.

If --vc-enable-gatk-acceleration 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).

If --vc-remove-all-soft-clips is set to true, the variant caller does not use soft clips of reads to determine variants.

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.

If --vc-enable-decoy-contigs is set to true, variant calls on the decoy contigs are enabled. The default value is false.

The –vc-enable-phasing option enables variants to be phased when possible. The default value is true.

Sets the maximum distance between phased variants to be combined. The default value is 0, which disables the option.