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%. On the other hand, non-cancer post-zygotic mosaic variants have typical allele frequencies (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 ideintified by a MOSAIC flag in the VCF INFO field.

When the mosaic detection is enabled, 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. MOSAIC tagged variants with QUAL smaller than 3 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.

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

Command line options

• --vc-enable-mosaic-detection

  Set to true to enable mosaic detection with mosaic AF filter threshold set to 0.0. Set to false to disable mosaic detection. The default is true with mosaic AF filter threshold set to 0.2.

• --vc-mosaic-af-filter-threshold

  Set the allele frequency 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 when the germline variant caller is enabled. The AF default threshold is set to 0.0 when the mosaic detection mode is enabled with --vc-enable-mosaic-detection=true.

• --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 3.0.

• --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

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

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 4.2 Mosaic Detection Mode	--enable-variant-caller=true --vc-enable-mosaic-detection=true	0.4	Yes	Yes (Full)	0%