Unique Molecular Identifiers Support

To optimize variant calling for different UMI use cases, use the following two batch modes. Both options are false by default. Enable UMI variant calling by setting one of them to true.

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--vc-enable-umi-solid—The VC UMI solid mode is optimized for solid tumors with post collapsed coverage rates of ~200—300X and target allele frequencies of 5% and higher.

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--vc-enable-umi-liquid—The liquid biopsy pipeline is not equivalent to liquid tumor mode. The liquid biopsy pipeline starts from a regular blood sample and looks for low VAF somatic variants from tumor cell free DNA floating in the blood. This type of test enables tumor profiling (diagnosis/biomarker identification) from plasma rather than from tissue, which requires an invasive biopsy. The VC UMI liquid mode is optimized for a liquid biopsy pipeline with post collapsed coverage rates of ~2000–2500X and target allele frequencies of 0.4% and higher.

These batch settings do not include the vc-systematic-noise filter. DRAGEN recommends adding the filter. For more information, see Systematic Noise Filtering.

In UMI pipelines, DRAGEN can estimate nucleotide mutation biases, such as oxidation and deamination artifacts that might exist upstream of the sequencing system on a per sample basis. During variant calling, DRAGEN corrects the biases.

To enable this feature, use --vc-target-bed, which also specifies the target regions for variant calling, or --vc-snp-error-cal-bed. If using --vc-snp-error-cal-bed, specify the regions from which to estimate nucleotide substitution bias if different from the target BED file or if a target BED file is not specified. If a third-party tool is used to produce the collapsed reads, then configure the tool so that the base call quality scores quantify the error shown on the sequencing system only. DRAGEN uses this error estimation to account for errors upstream of the sequencing system.