Overview - Upstream GATK
The CGAP Pipelines module for upstream processing with GATK (https://github.com/dbmi-bgm/cgap-pipeline-upstream-GATK) is our open-source solution 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.
Both the WES and WGS configurations are mostly based on bwa and GATK4, following GATK best practices.
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_gatk image is primarily for reads alignment and post-processing of the aligned reads.
This image contains (but is not limited to) the following software packages:
- gatk (4.2.6.1)
- picard (2.26.11)
- samtools (1.9)
- bwa (0.7.17)
