samtools-coverage(1)

NAME
samtools-coverage - produces a histogram or table of coverage per chromosome

SYNOPSIS

samtools coverage [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]]

DESCRIPTION

Computes the coverage at each position or region and draws an ASCII-art histogram or tabulated text.

Coverage is defined as the percentage of positions within each bin with at least one base aligned against it.

The tabulated form uses the following headings.

rname | Reference name / chromosome
startpos | Start position
endpos | End position (or sequence length)
numreads | Number reads aligned to the region (after filtering)
covbases | Number of covered bases with depth >= 1
coverage | Percentage of covered bases [0..100]
meandepth | Mean depth of coverage
meanbaseq | Mean baseQ in covered region
meanmapq | Mean mapQ of selected reads

OPTIONS

Input options:

-b, --bam-list FILE
    List of input BAM files, one file per line [null]

-l, --min-read-len INT
    Ignore reads shorter than INT base pairs [0]

-q, --min-MQ INT
    Minimum mapping quality for an alignment to be used [0]

-Q, --min-BQ INT
    Minimum base quality for a base to be considered [0]

--rf, --incl-flags STR|INT
    Required flags: skip reads with mask bits unset [null]

--ff, --excl-flags STR|INT
    Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]

-d, --depth INT
    Maximum allowed coverage depth [1000000]. If 0, depth is set to the maximum integer value effectively removing any depth limit.

Output options:

-m, --histogram
    Show histogram instead of tabular output.

-D, --plot-depth
    As above but displays the depth of coverage instead of the percent of coverage. This option can be used to visualize copy number variations in the terminal.

-A, --ascii
    Show only ASCII characters in histogram using colon and fullstop for full and half height characters.

-o, --output FILE
    Write output to FILE [stdout].

-H, --no-header
    Don't print a header in tabular mode.

-w, --n-bins INT
    Number of bins in histogram. [terminal width - 40]

-r, --region REG
    Show specified region. Format: chr:start-end.

-h, --help
    Shows command help.

EXAMPLES

Running coverage in tabular mode, on a specific region, with tabs shown as spaces for clarity in this man page.

    samtools coverage -r chr1:1M-12M input.bam

    #rname  startpos  endpos    numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
    chr1    1000000   12000000  528695    1069995   9.72723   3.50281    34.4       55.8

An example of the histogram output is below, with ASCII block characters replaced by "#" for rendering in this man page.

    samtools coverage -A -w 32 -r chr1:1M-12M input.bam

    chr1 (249.25Mbp)
    >  24.19% | .                              | Number of reads: 528695
    >  21.50% |::                              |     (132000 filtered)
    >  18.81% |::                              | Covered bases:   1.07Mbp
    >  16.12% |::                           :  | Percent covered: 9.727%
    >  13.44% |::  :  .       ::            : :| Mean coverage:   3.5x
    >  10.75% |:: ::  :       ::          : : :| Mean baseQ:      34.4
    >   8.06% |:::::  :       ::        : : : :| Mean mapQ:       55.8
    >   5.37% |::::: ::      :::      : ::::: :|
    >   2.69% |::::: :::     :::  ::: :::::::::| Histo bin width: 343.8Kbp
    >   0.00% |:::::::::::. :::::::::::::::::::| Histo max bin:   26.873%
            1.00M     4.44M     7.87M       12.00M

    samtools coverage  -m -r 'chr1:24500000-25600000' --plot-depth -w 32 -A input.bam

    chr1 (249.25Mbp)
    >    38.8 |            .:::::::            | Number of reads: 283218
    >    34.5 |            ::::::::            |     (3327 filtered)
    >    30.2 |           :::::::::.           | Covered bases:   1.10Mbp
    >    25.9 |.:::::.:.::::::::::::::::::::::.| Percent covered: 99.83%
    >    21.6 |::::::::::::::::::::::::::::::::| Mean coverage:   33.2x
    >    17.2 |::::::::::::::::::::::::::::::::| Mean baseQ:      37.2
    >    12.9 |::::::::::::::::::::::::::::::::| Mean mapQ:       59.3
    >     8.6 |::::::::::::::::::::::::::::::::|
    >     4.3 |::::::::::::::::::::::::::::::::| Histo bin width: 34.5Kbp
    >     0.0 |::::::::::::::::::::::::::::::::| Histo max cov:   43.117
            24.50M    24.84M    25.19M      25.60M

AUTHOR

Written by Florian P Breitwieser.

SEE ALSO
samtools(1), samtools-depth(1),

Samtools website: <http://www.htslib.org/>