Mosaic Detection

The default mode of the small variant caller has been optimized to detect germline variants with typical AFs of 0%, 50% or 100%. Non-cancer post-zygotic mosaic variants have typical allele fraction (AFs) lower than 50% and therefore more challenging to find with the default small variant caller. To improve sensitivity of low AF calls, a new machine learning (ML) model trained using read and context evidence from low AF calls is used. This allows the model to identify variants down to approximately 5% AF on 35x WGS and 3% AF on 300x WGS. The mosaic ML model is applied to all calls that are rejected by the germline model and variants detected with the mosaic detection are identified by a MOSAIC flag in the VCF INFO field.

MOSAIC tagged variants with QUAL smaller than 3.0103 are filtered with the MosaicHardQUAL filter.

We provide an optional MosaicLowAF filtering option to filter MOSAIC tagged variants with AF smaller than the AF threshold. The threshold for this filter can be set with the --vc-mosaic-af-filter-threshold option. The default value for the mosaic AF filter threshold is set to 0.2 if the median depth of the sample detected by the ploidy caller is <= 100x and 0.1 if the detected depth is >100x. All MOSAIC variants can be reported, regardless of their AF, with the --vc-mosaic-af-filter-threshold=0 option. For haploid regions, we apply separate handling that uses a threshold of 0.75 for assigning MOSAIC tags. Please refer to the Ploidy Support section for more details.

Furthermore, the output of MOSAIC tagged calls can be restricted using an optional target BED provided with the --vc-mosaic-target-bed option.

High Sensitivity Mosaic detection (Alpha)

The DRAGEN high sensitivity mosaic detection is designed to lower the limit of detection in high-depth datasets to approximately 1.5% AF and it can be enabled with --vc-enable-high-sensitivity-mosaic-detection=true. We suggest enabling the high hensitivity mosaic detection when interested in finding very low AF variants in high-depth samples (>=200x). Enabling high-sensitivity mosaic detection in DRAGEN will increase runtime by approximately 20–25%.

Note: Internal parameters of DRAGEN are changed from the default settings when the high sensitivity mosaic detection is enabled. This directly affects both the germline and mosaic small variant calling pipelines. Therefore, a direct comparison of the VCF files generated could highlight differences in the variant calls scores, as well as variants private to one VCF (even among non MOSAIC tagged calls).

Command line options

• --vc-enable-mosaic-detection

  Set to true to enable mosaic detection. Set to false to disable mosaic detection.

• --vc-mosaic-af-filter-threshold

  Set the allele fraction threshold for the application of the MosaicLowAF filter to mosaic calls. All MOSAIC tagged variants with AF smaller than the AF threshold are filtered with the MosaicLowAF filter. The default mosaic AF filter threshold is set to 0.2 if the median depth of the sample detected by the ploidy caller is <= 100x and 0.1 if the detected depth is > 100x.

• --vc-mosaic-qual-filter-threshold

  Set the QUAL threshold for the application of the MosaicHardQUAL filter to mosaic calls. All MOSAIC tagged variants with QUAL smaller than the threshold QUAL are filtered with the MosaicHardQUAL filter. The default mosaic QUAL filter threshold is set to 3.0103.

• --vc-mosaic-target-bed

  Optional target BED file to restrict the output of MOSAIC tagged variant calls only in the specified regions.

Comparison with DRAGEN 4.2 High Sensitivity Mode and DRAGEN v4.3 Mosaic

Small variant calling features comparison between default germline small variant caller and mosaic detection mode in DRAGEN 4.2, DRAGEN 4.3 and DRAGEN 4.4

Tag	Name	Command line options	QUAL threshold	MAPQ0	Mosaic Detection	Mosaic AF filter threshold
4.2	DRAGEN 4.2 default Small Variant Caller	--enable-variant-caller=true	3	No	No	N/A
4.2 HSM	DRAGEN 4.2 High Sensitivity Mode	--enable-variant-caller=true --vc-enable-high-sensitivity-mode=true	0.4	Yes	Yes (Alpha)	N/A
4.3	DRAGEN 4.3 default Small Variant Caller	--enable-variant-caller=true	3	Yes	Yes (Full)	20%
4.3 Mosaic	DRAGEN 4.3 Mosaic Detection Mode	--enable-variant-caller=true --vc-enable-mosaic-detection=true	0.4	Yes	Yes (Full)	0%
4.4	DRAGEN 4.4 default Small Variant Caller	--enable-variant-caller=true	3.0103	Yes	Yes (Full)	20% if depth <=100x, 10% otherwise
4.4	DRAGEN 4.4 default Small Variant Caller	--enable-variant-caller=true --vc-enable-mosaic-detection=true	3.0103	Yes	Yes (Full)	20% if depth <=100x, 10% otherwise
4.4 Mosaic	DRAGEN 4.4 Mosaic Detection Mode	--enable-variant-caller=true --vc-enable-mosaic-detection=true --vc-mosaic-af-filter-threshold=0	3.0103	Yes	Yes (Full)	0%

Comparison with DRAGEN 4.3 command line behavior

The command line behavior of --vc-enable-mosaic-detection=true has changed between DRAGEN 4.3 and DRAGEN 4.4. In DRAGEN 4.3, explicitly setting --vc-enable-mosaic-detection=true caused two changes to default behavior:

1. The hard filter QUAL threshold for both SNPs and INDELs is lowered to 0.4 in this mode to allow low AF calls to be set as PASS in the FILTER field.

2. The mosaic AF filter threshold is set to 0.0.

In DRAGEN 4.4, to improve the user experience, both these changes have been decoupled from the --vc-enable-mosaic-detection=true option, therefore the user can report all MOSAIC variants, regardless of their AF, with the --vc-mosaic-af-filter-threshold=0 option.