BEDTools.coverage (v1) BETA

This module is currently in beta release. The module and/or documentation may be incomplete.

Computes the depth and breadth of coverage of features in file A across the features in file B.

Author: Chet Birger, Broad Institute

Contact: gp-help@broadinstitute.org

Algorithm Version:

Introduction

BEDTools.coverage computes both the depth and breadth of coverage of features in file A across the features in file B.  BEDTools.coverage not only counts the number of features that overalp an interval in file B, it also computes the fraction of bases in the B interval that were overlapped by one or more features; hence, the bread of coverage for each interval in B.

References

BEDTools coverage online documentation

Parameters

Name Description
input file A  Input BED/GFF/VCF file A (-a)
bam input file A  Input BAM file A. (-abam)
input file B * Input BED/GFF/VCF file B (-b)
force strandedness  Force strandedness; that is, only merge features that are on the same strand. (-s)
report histogram  Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B. (-hist)
report depth  Report the depth at each position in each B feature. (-d)
split  Treat split BAM or BED12 entries as distinct BED interfals when computing coverage. (-split)
output filename * Output filename

* - required

Input Files

  1. input file A
    The first of two BED-, GFF- or VCF-formatted files containing annotation track data.  BEDTools.coverage computes the coverage of features in input file A across the features in input file B.
  2. input file B
    The second of two BED-, GFF- or VCF-formated files containing annotation track data.  BEDTools.coverage computes the coverage of features in input file A across the features in input file B.

Output Files

  1. output filename
    After the coordinates of each feature in B, the output file lists:
    1. The number of features in A that overalapped (by at least one base pair) the B interval.
    2. The number of bases in B that had non-zero coverage from feature in A
    3. The length of the entry in B
    4. The fraction of bases in B that had non-zero coverage from features in A

 

Platform Dependencies

Task Type:
ChIP-Seq

CPU Type:
any

Operating System:
any

Language:
C++

Version Comments

Version Release Date Description
1 2013-12-23 initial Beta version