Skip to content

Bed Merge Specifications

Process Details

  • Name: bed merge
  • Process UUID: 20bdd506-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process performs comprehensive BED file processing by sorting genomic intervals, extending them by a fixed distance, merging overlapping regions, and adding unique identifiers. It is designed to consolidate overlapping or nearby genomic features into unified intervals while maintaining proper genomic coordinate formatting.

This process is implemented in Bash, utilizing bedtools for genomic interval operations.

Key Functionality

  • Interval Sorting: Sorts BED file entries by genomic coordinates to ensure proper ordering
  • Interval Extension: Extends each genomic interval by 100 base pairs in both directions using genome size constraints
  • Overlap Merging: Consolidates overlapping or adjacent intervals into single unified regions
  • Identifier Assignment: Adds unique identifiers to merged intervals in the format "chromosome_start_end"

Input/Output Specification

Inputs

Required Inputs

  • BED File

    • Description: Input BED format file containing genomic intervals to be processed
    • Format: BED

  • Genome Sizes File

    • Description: Reference file containing chromosome names and their corresponding lengths for boundary checking during interval extension
    • Format: sizes

Outputs

  • Merged BED File
    • Description: Processed BED file containing sorted, extended, and merged genomic intervals with added unique identifiers
    • Format: BED

Parameters & Settings

This process uses fixed parameters and does not have user-configurable options in the Foundry UI.

References & Resources

  • Tool Documentation: This process utilizes standard bedtools utilities (bedtools sort, bedtools slop, bedtools merge) for genomic interval manipulation