Overview - Upstream Sentieon
The CGAP Pipelines module for upstream processing with Sentieon (https://github.com/dbmi-bgm/cgap-pipeline-upstream-sentieon) is our license-based option for processing Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) datasets.
The pipeline takes paired-end fastq files and produces analysis-ready bam files that can be used by any of the CGAP Pipelines downstream modules (e.g., SNV Germline and SV Germline).
The pipeline is based on hg38/GRCh38 genome build and is optimized for 30x coverage for WGS data and 90x coverage for WES data. It has been tested with WGS data up to 80-90x coverage and WES data ranging from 20 to 200x coverage.
The pipeline is based on Sentieon implementation of bwa and GATK4 algorithms, following GATK best practices. Sentieon offers a faster and more computationally efficient implementation of the original algorithms.
Note: If the user wants to provide cram files as input, they must first be converted to paired-end fastq files using the CGAP Pipelines base module (https://github.com/dbmi-bgm/cgap-pipeline-base).
Docker Image
The Dockerfiles provided in this GitHub repository can be used to build public docker images.
If built through portal-pipeline-utils pipeline_deploy command (https://github.com/dbmi-bgm/portal-pipeline-utils), private ECR images will be created for the target AWS account.
The upstream_sentieon image contains (but is not limited to) the following software packages:
- Sentieon (202112.01)
- samtools (1.9)
Pipeline Flow
Our implementation offers an end-to-end solution to process raw sequencing data, producing an analysis-ready bam file as described here.
For more details see the documentation for Upstream GATK module.
This pipeline follows the same logic and structure and simply replaces some of the open-source software with the equivalent Sentieon implementation.
The overall flow of the pipeline is shown below:
