The DRAGEN Somatic V2 Pipeline allows ultra-rapid analysis of next-generation sequencing (NGS) data to identify cancer-associated mutations. DRAGEN is able to call SNPs and INDELs from both matched tumor/normal pairs and tumor-only samples. DRAGEN produces rapid results while achieving a level of accuracy greater than top somatic variant callers.
DRAGEN Somatic Pipeline V2
The DRAGEN V2 Somatic Pipeline offers flexible data analysis to suit different needs. It accepts FASTQ, BAM/CRAM, and BCL files and supports NGS input from whole genome, whole exome, and targeted cancer panels. The somatic pipeline calls SNPs and INDELs while also reporting allele frequency. The somatic pipeline can be automated using the DRAGEN Workflow Management System for ease of use and bulk sample processing. It is available onsite, in the Cloud, or as a hybrid Cloud solution.
In the tumor/normal pipeline, both samples go through identical processing steps and are input into the variant caller, where germline variants are excluded to produce a VCF file specific for tumor mutations.
The tumor-only pipeline lacks a matching normal sample and produces a VCF file containing both somatic and germline variants. Users have two options for refining the data to identify somatic variants: 1) Input a panel-of-normals dataset as a germline filter in the variant caller; 2) Compare the output VCF to publicly available databases of germline SNPs and INDELs to remove known germline variants.
The ICGC-TCGA DREAM Mutation Calling Challenge was a contest to find the most accurate tool for detecting variants in synthetically generated mutation datasets. The DRAGEN Somatic V2 Variant Caller was benchmarked against the top-performing variant callers from the DREAM Challenge and outperformed them for both SNP and INDEL accuracy. In the chart below, the winning submission of the DREAM Challenge for synthetic dataset 4 is highlighted in grey; DRAGEN Somatic V2 Pipeline is in blue.
A 2015 study (Alioto et al., Nature Communications) compared multiple somatic variant calling tools for accuracy in calling SNPs and INDELs from a medulloblastoma tumor sample. A curated gold set was used to benchmark performance. The DRAGEN V2 Somatic Variant Caller analyzed the same FASTQs as the other tools and produced better measures of accuracy for SNPs and INDELs. The top performing submissions are highlighted in grey; DRAGEN V2 in blue