5.9 coverageBed

coverageBed computes both the depth and breadth of coverage of features in file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. One advantage that coverageBed offers is that it not only counts the number of features that overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features. Thus, coverageBed also computes the breadth of coverage for each interval in B.

5.9.1 Usage and option summary

Usage:

coverageBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>

Option	Description
-abam	BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use “stdin” if passing A with a UNIX pipe: For example: samtools view -b <BAM> | intersectBed -abam stdin -b genes.bed
-s	Force strandedness. That is, only features in A are only counted towards coverage in B if they are the same strand. By default, this is disabled and coverage is counted without respect to strand.
-hist	Report a histogram of coverage for each feature in B as well as a summary histogram for _all_ features in B. Output (tab delimited) after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth
-d	Report the depth at each position in each B feature. Positions reported are one based. Each position and depth follow the complete B feature.
-split	Treat “split” BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR “N” and “D” operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).

5.9.2 Default behavior

After each interval in B, coverageBed will report:

1. The number of features in A that overlapped (by at least one base pair) the B interval.
2. The number of bases in B that had non-zero coverage from features 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.

Below are the number of features in A (N=...) overlapping B and fraction of bases in B with coverage.

Chromosome  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BED FILE B  ***************     ***************     ******    **************

BED File A  ^^^^ ^^^^              ^^             ^^^^^^^^^    ^^^ ^^ ^^^^
              ^^^^^^^^                                      ^^^^^ ^^^^^ ^^

Result      [  N=3, 10/15 ]     [  N=1, 2/16 ]     [N=1,6/6]   [N=5, 11/12 ]

For example:

cat A.bed
chr1  10  20
chr1  20  30
chr1  30  40
chr1  100 200

cat B.bed
chr1  0   100
chr1  100 200
chr2  0   100

coverageBed -a A.bed -b B.bed
chr1  0   100  3  30  100 0.3000000
chr1  100 200  1  100 100 1.0000000
chr2  0   100  0  0   100 0.0000000

5.9.4 (-s)Calculating coverage by strand

Use the “-s” option if one wants to only count coverage if features in A are on the same strand as the feature / window in B. This is especially useful for RNA-seq experiments.

For example (note the difference in coverage with and without -s:

cat A.bed
chr1  10  20  a1  1  -
chr1  20  30  a2  1  -
chr1  30  40  a3  1  -
chr1  100 200 a4  1  +

cat B.bed
chr1  0   100 b1  1  +
chr1  100 200 b2  1  -
chr2  0   100 b3  1  +

coverageBed -a A.bed -b B.bed
chr1  0   100 b1  1  +  3  30  100  0.3000000
chr1  100 200 b2  1  -  1  100 100  1.0000000
chr2  0   100 b3  1  +  0  0   100  0.0000000

coverageBed -a A.bed -b B.bed -s
chr1  0   100 b1  1  +  0  0   100  0.0000000
chr1  100 200 b2  1  -  0  0   100  0.0000000
chr2  0   100 b3  1  +  0  0   100  0.0000000

5.9.5 (-hist)Creating a histogram of coverage for each feature in the B file

One should use the “-hist” option to create, for each interval in B, a histogram of coverage of the features in A across B.

In this case, each entire feature in B will be reported, followed by the depth of coverage, the number of bases at that depth, the size of the feature, and the fraction covered. After all of the features in B have been reported, a histogram summarizing the coverage among all features in B will be reported.

cat A.bed
chr1  10  20  a1  1  -
chr1  20  30  a2  1  -
chr1  30  40  a3  1  -
chr1  100 200 a4  1  +

cat B.bed
chr1  0   100 b1  1  +
chr1  100 200 b2  1  -
chr2  0   100 b3  1  +

coverageBed -a A.bed -b B.bed -hist
chr1  0   100 b1  1  +  0  70  100  0.7000000
chr1  0   100 b1  1  +  1  30  100  0.3000000
chr1  100 200 b2  1  -  1  100 100  1.0000000
chr2  0   100 b3  1  +  0  100 100  1.0000000
all   0   170 300 0.5666667
all   1   130 300 0.4333333

5.9.6 (-hist)Reporting the per-base of coverage for each feature in the B file

One should use the “-d” option to create, for each interval in B, a detailed list of coverage at each of the positions across each B interval.

The output will consist of a line for each one-based position in each B feature, followed by the coverage detected at that position.

cat A.bed
chr1  0  5
chr1  3  8
chr1  4  8
chr1  5  9

cat B.bed
chr1  0  10

coverageBed -a A.bed -b B.bed -d
chr1  0  10  B  1  1
chr1  0  10  B  2  1
chr1  0  10  B  3  1
chr1  0  10  B  4  2
chr1  0  10  B  5  3
chr1  0  10  B  6  3
chr1  0  10  B  7  3
chr1  0  10  B  8  3
chr1  0  10  B  9  1
chr1  0  10  B  10 0

5.9.7 (-split)Reporting coverage with spliced alignments or blocked BED features

As described in section 1.3.19, coverageBed will, by default, screen for overlaps against the entire span of a spliced/split BAM alignment or blocked BED12 feature. When dealing with RNA-seq reads, for example, one typically wants to only tabulate coverage for the portions of the reads that come from exons (and ignore the interstitial intron sequence). The -split command allows for such coverage to be performed.