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IGV BAM2TDF Converter Specifications

Process Details

  • Name: IGV BAM2TDF converter
  • Process UUID: 20bdccfa-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process converts BAM alignment files into TDF (Tiled Data Format) files optimized for visualization in the Integrative Genomics Viewer (IGV). The conversion enables efficient viewing of sequencing data coverage and alignment patterns across genomic regions at various zoom levels.

This process is implemented in Bash, which utilizes samtools for BAM file processing and IGV Tools for TDF conversion.

Key Functionality

  • BAM File Preparation: Automatically sorts and indexes BAM files if not already processed
  • TDF Conversion: Converts BAM files to TDF format using IGV Tools with configurable window sizes and extension factors
  • Paired-End Support: Handles both single-end and paired-end sequencing data with appropriate parameter adjustments

Input/Output Specification

Inputs

Required Inputs

  • Mate Information

    • Description: Sequencing mate pair configuration (single or paired-end)
    • Format: Value parameter

  • Mapped Reads

    • Description: Aligned sequencing reads in BAM format
    • Format: BAM files

  • Genome Sizes

    • Description: Chromosome sizes file containing genomic coordinates
    • Format: Sizes file

Outputs

  • TDF Output File
    • Description: Converted TDF file optimized for IGV visualization
    • Format: TDF file

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • IGV Window Size

    • Description: Window size for TDF binning and coverage calculation
    • Default value: Configurable via igv_window_size parameter

  • IGV Extension Factor

    • Description: Extension factor for read coverage calculation
    • Default value: Configurable via igv_extention_factor parameter

  • Nucleic Acid Type

    • Description: Type of sequencing data (DNA or RNA) affecting paired-end processing
    • Default value: Configurable via nucleicAcidType parameter

References & Resources

  • Tool Documentation: Contact the team for details on IGV Tools and samtools integration