Skip to content

Bedtools Coverage Specifications

Process Details

  • Name: bedtools_coverage
  • Process UUID: 20bdd66e-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process performs genomic coverage analysis by comparing BAM files against BED regions using bedtools. It checks for the presence of a comparison BED file, calculates coverage statistics for overlapping regions, and generates summary statistics showing the depth and breadth of coverage across specified genomic intervals.

This process is implemented in Bash.

Key Functionality

  • Coverage Calculation: Computes coverage statistics for genomic regions defined in BED files using aligned sequencing data from BAM files
  • Region Intersection: Identifies overlapping regions between BAM alignments and specified genomic intervals
  • Statistical Summarization: Generates grouped summary statistics showing coverage depth and fraction of bases covered per genomic region

Input/Output Specification

Inputs

Required Inputs

  • Compare BED File

    • Description: BED file containing genomic regions of interest for coverage analysis
    • Format: BED format

  • BED File

    • Description: Additional BED file for genomic interval definitions
    • Format: BED format

  • BAM Files

    • Description: Set of aligned sequencing data files for coverage calculation
    • Format: BAM format

Outputs

  • Coverage Summary
    • Description: Text file containing coverage statistics and summary data for analyzed genomic regions
    • Format: TXT format

Parameters & Settings

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

  • Bedtools Coverage Parameters

    • Description: bedtools Coverage parameters
    • Default value: -sorted -hist

  • Bedtools Intersect Optional Parameters

    • Description: bedtools Intersect optional parameters
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on bedtools usage and parameter configuration