Somatic mode

The DRAGEN Somatic Pipeline allows ultrarapid analysis of NGS data to identify cancer-associated mutations in somatic chromosomes. DRAGEN calls SNVs and indels from both matched tumor-normal pairs and tumor-only samples.

For the tumor-normal pipeline, both samples are analyzed jointly such that germline variants are excluded, generating an output specific to tumor mutations. The tumor-only pipeline produces a VCF file containing both germline and somatic variants that can be further analyzed to identify tumor mutations. For the tumor sample, both pipelines make no ploidy assumptions, enabling detection of low-frequency alleles.

The output, after multiple filtering dbSNP Annotationsteps, is in the form of a VCF file. Variants that fail the filtering steps are kept in the output VCF, with a FILTER annotation indicating which filtering steps have failed.

You can use somatic quality (SQ) as the primary metric to describe the confidence with which the caller made a somatic call. SQ is reported as a format field for the tumor sample. Variants with SQ score below the SQ filter threshold are filtered out using the weak_evidence tag. To trade off sensitivity against specificity, adjust the SQ filter threshold. Lower thresholds produce a more sensitive caller and higher thresholds produce a more conservative caller.