pybedtools.bedtool.BedTool.coverage

BedTool.coverage(*args, **kwargs)

Wraps bedtools coverage.

Note that starting in version 2.24.0, BEDTools swapped the semantics of the “a” and “b” files.

Example usage:

>>> a = pybedtools.example_bedtool('a.bed')
>>> b = pybedtools.example_bedtool('b.bed')
>>> c = b.coverage(a)
>>> c.head(3) 
chr1    155     200     feature5        0       -       2       45      45      1.0000000
chr1    800     901     feature6        0       +       1       1       101     0.0099010

For convenience, the file or stream this BedTool points to is implicitly passed as the -a argument to coverageBed

Original BEDTools help::

Tool:    bedtools coverage (aka coverageBed)
Version: v2.31.1
Summary: Returns the depth and breadth of coverage of features from B
         on the intervals in A.

Usage:   bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>

Options: 
        -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.

        -mean   Report the mean depth of all positions in each A feature.

        -s      Require same 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.

        -f      Minimum overlap required as a fraction of A.
                - Default is 1E-9 (i.e., 1bp).
                - FLOAT (e.g. 0.50)

        -F      Minimum overlap required as a fraction of B.
                - Default is 1E-9 (i.e., 1bp).
                - FLOAT (e.g. 0.50)

        -r      Require that the fraction overlap be reciprocal for A AND B.
                - In other words, if -f is 0.90 and -r is used, this requires
                  that B overlap 90% of A and A **also** overlaps 90% of B.

        -e      Require that the minimum fraction be satisfied for A OR B.
                - In other words, if -e is used with -f 0.90 and -F 0.10 this requires
                  that either 90% of A is covered OR 10% of  B is covered.
                  Without -e, both fractions would have to be satisfied.

        -split  Treat "split" BAM or BED12 entries as distinct BED intervals.

        -g      Provide a genome file to enforce consistent chromosome sort order
                across input files. Only applies when used with -sorted option.

        -nonamecheck    For sorted data, don't throw an error if the file has different naming conventions
                        for the same chromosome. ex. "chr1" vs "chr01".

        -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

        -bed    If using BAM input, write output as BED.

        -header Print the header from the A file prior to results.

        -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  Specify amount of memory to use for input buffer.
                Takes an integer argument. Optional suffixes K/M/G supported.
                Note: currently has no effect with compressed files.

Default Output:  
         After each entry in A, reports: 
           1) The number of features in B that overlapped the A interval.
           2) The number of bases in A that had non-zero coverage.
           3) The length of the entry in A.
           4) The fraction of bases in A that had non-zero coverage.