Perform alignment and variant calling for SNPs, small indels, and structural 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. This workflow performs read alignment, SNP and small indel, and structural variant calling steps on long read data. The workflow is designed for use with a variety of reference genomes, which are downloaded as part of workflow execution.
The workflow outputs both small and structural variant calls.
The long read pipeline is capable of processing either PacBio or Oxford Nanopore long reads. Either read type may be used as the
Long read FASTQ files, generated by either PacBio or Oxford Nanopore sequencers
Sample read groups
The name of the human reference genome build. (‘hg38_alt’, ‘hg38_gatk’, ‘hg38’, ‘hg38_noalt’, ‘hs38’, ‘b37_gatk’, ‘b37’, ‘hs37d5’, ‘hg19’, ‘ucsc_hg19’)
The DNAscope LongRead model file. If provided, small variant calls will be output
The LongReadSV model file
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 Sentieon long read germline pipeline outputs aligned reads and a long read structural variant VCF. If a DNAscope long read model is provided, it will also output a VCF containing SNPs and small indels.
Aligned and duplicate marked reads
Long read structural variant VCF
SNP and small indel call VCF; output if
The latest version of the Sentieon Docker image can be run by following the instructions listed here.