AddOrReplaceReadGroups Specifications
Process Details
- Name:
AddOrReplaceReadGroups - Process UUID:
f931hrv53okpmn1mk03w5oe5704pwd - Process Group:
gatk4
Overview
This process adds or replaces read group information in BAM files using GATK's AddOrReplaceReadGroups tool. Read groups are essential metadata that identify which reads belong to which sample, library, sequencing platform, and sequencing run. This information is critical for downstream variant calling and analysis workflows, as it allows tools to properly handle technical artifacts and batch effects that may be associated with different sequencing runs or platforms.
This process is implemented in Bash, which invokes GATK4 for read group manipulation.
Key Functionality
- Read Group Assignment: Adds or replaces read group tags (@RG) in BAM file headers and associated reads
- Sample Identification: Assigns sample name (RGSM) to identify which biological sample the reads originated from
- Library Tracking: Records library name (RGLB) to track which DNA/RNA library preparation was used
- Platform Documentation: Documents sequencing platform (RGPL), platform model (RGPM), and platform unit (RGPU) information
Input/Output Specification
Inputs
Required Inputs
- Mapped Reads
- Description: BAM files containing aligned sequencing reads that need read group information added or updated
- Format: BAM
Outputs
- Mapped Reads
- Description: BAM files with properly formatted read group information added to headers and reads
- Format: BAM
Parameters & Settings
The read group parameters are configured through the pipeline settings and include platform (RGPL), platform model (RGPM), and platform unit (RGPU) information that will be applied to the BAM files.
References & Resources
- Tool Documentation: GATK AddOrReplaceReadGroups
- Related Papers: McKenna A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303. DOI: 10.1101/gr.107524.110