Variant Caller Options

The following options control the variant caller stage.




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


[Optional] 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. The positions are zero-based. For example:

# header information
chr11 0 246920
chr11 255660 255661

If the reference span of the variant overlaps with any of the regions in the target BED, then the variant is output. If the reference span does not overlap, the variant is not output. For SNPs and Insertions, the reference span is 1 bp. For deletions, the reference span is the length of the deletion.


[Optional] Pads all target BED regions with the specified value. For example, if a BED region is 1:1000–2000 and the specified padding value is 100, the result 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.


Specifies the target coverage for downsampling. The default value is 500 for germline mode and 50 for somatic mode.


Set to true to run the in GATK mode. Enabling GATK mode using this option is concordant with GATK 3.7 in germline mode and GATK 4.0 in somatic mode.


Set to true to ignore soft-clipped bases during the haploytype assembly step.


Specifies a comma-separated list of contigs to skip during variant calling. This option can be set in the configuration file.


Set to true to enable variant calls on the decoy contigs. The default value is false.


Enable variants to be phased when possible. The default value is true.


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