Skip to content

README.md

Latest commit

 

History

History
101 lines (81 loc) · 3.58 KB

README.md

File metadata and controls

101 lines (81 loc) · 3.58 KB

Picard AddOrReplaceReadGroups Wrapper

A wrapper for Picard's AddOrReplaceReadGroups tool, providing a structured interface for adding or replacing read groups in BAM files.

Version

Current version: 1.0.0 (First stable release)

For a detailed list of changes, see the CHANGELOG.md.

Usage

For general information on how to use wrappers in Snakemake, please refer to the root README.md.

rule add_readgroups:
    input:
        "mapped.bam"
    output:
        "mapped_with_rg.bam"
    params:
        # Required Parameters
        ID="flow_cell.lane",        # Read Group ID
        LB="library_prep_1",        # Read Group Library
        PL="ILLUMINA",              # Read Group platform
        PU="flow_cell.1.lane",      # Read Group platform unit
        SM="sample1",               # Read Group sample name
        
        # Optional Parameters
        CN="sequencing_center",     # Read Group sequencing center
        PM="NextSeq2000",           # Read Group platform model
        
        # Additional Parameters
        validation_stringency="LENIENT",  # Validation stringency
        create_index=True,                # Create BAM index
        compression_level=5,              # BAM compression level
        extra="",                         # Additional parameters
        version="1.0.0"                   # Wrapper version
    wrapper:
        "file://path/to/damlab-wrappers/picard/addorreplacereadgroups"

Parameters

Required Parameters

  • ID (str): Read Group ID (required)
  • LB (str): Read Group Library (required)
  • PL (str): Read Group platform (e.g. ILLUMINA, SOLID) (required)
  • PU (str): Read Group platform unit (required)
  • SM (str): Read Group sample name (required)

Optional Parameters

  • CN (str, optional): Read Group sequencing center name
  • DS (str, optional): Read Group description
  • DT (str, optional): Read Group run date
  • FO (str, optional): Read Group flow order
  • KS (str, optional): Read Group key sequence
  • PG (str, optional): Read Group program group
  • PI (int, optional): Read Group predicted insert size
  • PM (str, optional): Read Group platform model
  • validation_stringency (str, optional): Validation stringency (SILENT, LENIENT, STRICT). Defaults to None.
  • create_index (bool, optional): Create BAM index. Defaults to True.
  • compression_level (int, optional): BAM compression level (0-9). Defaults to None.
  • extra (str, optional): Additional parameters to pass to Picard. Defaults to "".
  • version (str, optional): Specify a version of the wrapper to use.

Input

  • BAM file
    • Must be a valid BAM file
    • Can be sorted or unsorted
    • Can have existing read groups or not

Output

  • BAM file with read groups added/replaced
    • Contains all reads from input BAM
    • Read groups updated according to parameters
    • BAM index created (if create_index=True)

Error Handling

The wrapper includes comprehensive error handling for:

  • Missing input files
  • Missing required parameters
  • Invalid parameter values
  • Picard execution errors

Notes

  • Read group parameters are critical for downstream analysis
  • The ID parameter must be unique for each read group
  • The SM parameter should match the sample name used in variant calling
  • Validation stringency can be adjusted if input BAM has issues

Author

  • Will Dampier, PhD

Software Requirements

  • Picard (tested with v2.27.5)
  • Java runtime environment

License

This project is licensed under the MIT License - see the LICENSE file for details.