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UCSC BAM2BigWig Converter Specifications

Process Details

  • Name: UCSC BAM2BigWig converter
  • Process UUID: 20bdcfac-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process converts BAM files to BigWig format for enhanced genome browser visualization. The conversion enables efficient visualization of sequencing coverage data in genome browsers by creating compressed, indexed files that support fast random access to genomic regions.

This process is implemented in Bash, which utilizes samtools for BAM file processing, bedtools for coverage calculation, and UCSC's wigToBigWig utility for final format conversion.

Key Functionality

  • BAM File Preparation: Automatically sorts and indexes BAM files if not already processed
  • Coverage Calculation: Generates genome-wide coverage data using bedtools genomecov with split-read support
  • Format Conversion: Converts coverage data to BigWig format using UCSC wigToBigWig utility with optimized parameters

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads

    • Description: BAM files containing aligned sequencing reads
    • Format: BAM

  • Genome Sizes

    • Description: Chromosome sizes file specifying the length of each chromosome in the reference genome
    • Format: sizes

Outputs

  • BigWig File
    • Description: Compressed, indexed coverage file suitable for genome browser visualization
    • Format: BigWig (.bw)

References & Resources

  • Tool Documentation: Contact the team for details on the conversion pipeline implementation