Compare tumor/normal samples and call somatic variants using Sentieon.
This workflow implements the Sentieon® Genomics software, a set of software tools that perform highly accurate and computationally efficient analysis of genomic data. For both tumor and normal samples the workflow performs read alignment, deduplication and BQSR. The workflow then calls somatic variants on each sample, identifying potential sites where the cancer genome data displays somatic variations relative to the normal genome, and calculates genotypes at those sites. Finally, the variants are filtered.
The workflow is designed for use with a variety of reference genomes, which are downloaded as part of workflow execution.
This workflow was developed by the Sentieon development and is written in Workflow Description Language (WDL). Further documentation can be found here. TNseq®-specific documentation may be found here.
Both tumor and optionally normal sample reads are input. Each sample’s inputs will be separately aligned and corrected, before being combined during somatic variant calling and filtering
R1 fastq files for the tumor sample
R2 fastq files for the tumor sample
Read groups for the tumor sample
R1 fastq files for the normal sample
R2 fastq files for the normal sample
Read groups for the normal sample
The name of the human reference genome build. (‘hg38_alt’, ‘hg38_gatk’, ‘hg38’, ‘hg38_noalt’, ‘hs38’, ‘b37_gatk’, ‘b37’, ‘hs37d5’, ‘hg19’, ‘ucsc_hg19’)
The panel of normals VCF file
The panel of normals VCF index file
The germline VCF file
The germline VCF index file
The VCF file of germline sites for contamination detection
The VCF index file of germline sites for contamination detection
Your account’s AWS canonical user ID. Used to acquire a Sentieon license
Sentieon docker image
Number of vCPUs to allocate for the task 
Memory to allocate for the task [64 GiB]
The main output of the pipeline is a VCF containing somatic variant calls. Various metrics and plots are also produced.
Somatic variant calls output by TNfilter
Index for the
Each output listed here will be produced for both the tumor sample and the normal sample, if a normal sample is provided. Normal sample outputs are produced if any normal sample fastqs are provided (i.e. if
The latest version of the Sentieon Docker image can be run by following the instructions listed here.