Somatic Mode

The DRAGEN Somatic Pipeline allows ultrarapid analysis of Next-Generation Sequencing (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 using a probability model that considers the possibility of somatic variants, germline variants, and various systematic noise artifacts. When considering somatic variants, DRAGEN does not make any ploidy assumptions, which enables detection of low-frequency alleles. For loci with coverage up to 100x in the tumor sample, DRAGEN has a limit of detection at variant allele frequencies of 5%. The limit scales with increasing depth on a per-locus basis and halves every time the coverage doubles beyond 100x.

For the tumor-normal pipeline, both samples are analyzed jointly. DRAGEN assumes that germline variants and systematic noise artifacts would be shared by both samples, whereas somatic variants would be present only in the tumor sample. Only somatic variants are reported. To detect systematic noise artifacts, DRAGEN recommends that the coverage in the normal sample be at least half of the coverage in the tumor sample.

After multiple filtering steps, the output is generated as a VCF file. Variants that fail the filtering steps are kept in the output VCF. The variants include a FILTER annotation that indicates 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 a Phred-scaled posterior probability reported as a format field for the tumor sample (exception: for homozygous reference calls in gVCF mode it is instead a likelihood ratio, analogous to hom-ref GQ as described in the germline section). 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. Lowering a threshold produces a more sensitive caller and a higher thresholds produces a more conservative caller. If performing tumor-normal analysis, the SQ field for the normal sample contains the Phred-scaled posterior probability that a putative call is a germline variant.