Commit a0778bfc authored by arq5x's avatar arq5x
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update coverage docs

parent c6210147
......@@ -3,67 +3,99 @@
###############
*coverage*
###############
**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.
The ``bedtools coverage`` tool computes both the *depth* and *breadth* of coverage of features in file B on the features
in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments (file B) across 1
kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that ``bedtools coverage``
offers is that it not only *counts* the number of features that overlap an interval in file A, it also
computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus,
``bedtools coverage`` also computes the *breadth* of coverage observed for each interval in A.
==========================================================================
Usage and option summary
==========================================================================
Usage:
.. note::
::
If you are trying to compute coverage for very large files and are having trouble
with excessive memory usage, please presort your data by chromosome and
then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
for BED files) and then use the ``-sorted`` option. This invokes a
memory-efficient algorithm designed for large files.
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:
.. important::
As of version 2.24.0, the `coverage` tool can accept multiple files for
the `-b` option. This allows one to identify overlaps between a single
query (`-a`) file and multiple database files (`-b`) at once!
| 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).
=========================== ===============================================================================================================================================================================================================
.. seealso::
:doc:`../tools/intersect`
:doc:`../tools/genomecov`
===============================
Usage and option summary
===============================
**Usage**:
::
bedtools coverage [OPTIONS] -a <FILE> \
-b <FILE1, FILE2, ..., FILEN>
**(or)**:
::
coverageBed [OPTIONS] -a <FILE> \
-b <FILE1, FILE2, ..., FILEN>
=========================== =========================================================================================================================================================
Option Description
=========================== =========================================================================================================================================================
**-a** BAM/BED/GFF/VCF file "A". Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
**-b** One or more BAM/BED/GFF/VCF file(s) "B". Use "stdin" if passing B with a UNIX pipe.
**NEW!!!**: -b may be followed with multiple databases and/or wildcard (*) character(s).
**-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> | bedtools intersect -abam stdin -b genes.bed. **Note**: no longer necessary after version 2.19.0
**-hist** | Report a histogram of coverage for each feature in A as well as a summary histogram for _all_ features in A.
| Output (tab delimited) after each feature in A:
| 1) depth
| 2) # bases at depth
| 3) size of A
| 4) % of A at depth
**-d** Report the depth at each position in each A feature. Positions reported are one based. Each position and depth follow the complete A feature.
**-counts** Only report the count of overlaps, don't compute fraction, etc. Restricted by -f and -r.
**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
**-split** Treat "split" BAM (i.e., having an "N" CIGAR operation) or BED12 entries as distinct BED intervals.
**-sorted** For very large B files, invoke a "sweeping" algorithm that requires position-sorted (e.g., ``sort -k1,1 -k2,2n`` for BED files) input. When using -sorted, memory usage remains low even for very large files.
**-g** Specify a genome file the defines the expected chromosome order in the input files for use with the ``-sorted`` option.
**-header** Print the header from the A file prior to results.
**-sortout** When using *multiple databases* (`-b`), sort the output DB hits for each record.
**-nobuf** Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.
**-iobuf** Follow with desired integer size of read buffer. Optional suffixes `K/M/G` supported. **Note**: currently has no effect with compressed files.
=========================== =========================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
After each interval in B, **coverageBed** will report:
After each interval in A, ``bedtools coverage`` 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.
1) The number of features in B that overlapped (by at least one base pair) the A interval.
2) The number of bases in A that had non-zero coverage from features in B.
3) The length of the entry in A.
4) The fraction of bases in A that had non-zero coverage from features in B.
Below are the number of features in A (N=...) overlapping B and fraction of bases in B with coverage.
Below are the number of features in B (N=...) overlapping A and fraction of bases in A with coverage.
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BED FILE B *************** *************** ****** **************
BED FILE A *************** *************** ****** **************
BED File A ^^^^ ^^^^ ^^ ^^^^^^^^^ ^^^ ^^ ^^^^
BED File B ^^^^ ^^^^ ^^ ^^^^^^^^^ ^^^ ^^ ^^^^
^^^^^^^^ ^^^^^ ^^^^^ ^^
Result [ N=3, 10/15 ] [ N=1, 2/15 ] [N=1,6/6] [N=6, 12/14 ]
......@@ -71,20 +103,20 @@ Below are the number of features in A (N=...) overlapping B and fraction of base
For example:
::
.. code-block:: bash
$ cat A.bed
chr1 0 100
chr1 100 200
chr2 0 100
cat A.bed
$ cat B.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
$ bedtools coverage -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
......@@ -95,57 +127,58 @@ For example:
``-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.
feature / window in A. This is especially useful for RNA-seq experiments.
For example (note the difference in coverage with and without **-s**:
::
.. code-block:: bash
$ cat A.bed
chr1 0 100 b1 1 +
chr1 100 200 b2 1 -
chr2 0 100 b3 1 +
cat A.bed
$ cat B.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
$ bedtools coverage -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
$ bedtools coverage -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
==========================================================================
``-hist`` Creating a histogram of coverage for each feature in the B file
``-hist`` Creating a histogram of coverage for each feature in the A 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.
One should use the "**-hist**" option to create, for each interval in A, a histogram of coverage of the
features in B across A.
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.
In this case, each entire feature in A 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 A have
been reported, a histogram summarizing the coverage among all features in A will be reported.
::
.. code-block:: bash
cat A.bed
$ cat A.bed
chr1 0 100 b1 1 +
chr1 100 200 b2 1 -
chr2 0 100 b3 1 +
$ cat B.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
$ bedtools coverage -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
......@@ -154,28 +187,27 @@ been reported, a histogram summarizing the coverage among all features in B will
all 1 130 300 0.4333333
===========================================================================
``-d`` Reporting the per-base of coverage for each feature in the B file
``-d`` Reporting the per-base of coverage for each feature in the A 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.
One should use the "**-d**" option to create, for each interval in A, a detailed list of coverage at each of the
positions across each A interval.
The output will consist of a line for each one-based position in each B feature, followed by the coverage
The output will consist of a line for each one-based position in each A feature, followed by the coverage
detected at that position.
::
.. code-block:: bash
$ cat A.bed
chr1 0 10
cat A.bed
$ cat B.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
$ bedtools coverage -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
......@@ -186,14 +218,3 @@ detected at that position.
chr1 0 10 B 8 3
chr1 0 10 B 9 1
chr1 0 10 B 10 0
=============================================================================
``-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.
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