samtools-coverage(1) Bioinformatics tools samtools-coverage(1)

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

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

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

Input options:

List of input BAM files, one file per line [null]
Ignore reads shorter than INT base pairs [0]
Minimum mapping quality for an alignment to be used [0]
Minimum base quality for a base to be considered [0]
Required flags: skip reads with mask bits unset [null]
Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
Maximum allowed coverage depth [1000000]. If 0, depth is set to the maximum integer value effectively removing any depth limit.

Output options:

Show histogram instead of tabular output.
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.
Show only ASCII characters in histogram using colon and fullstop for full and half height characters.
Write output to FILE [stdout].
Don't print a header in tabular mode.
Number of bins in histogram. [terminal width - 40]
Show specified region. Format: chr:start-end.
Shows command help.

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

Written by Florian P Breitwieser.

samtools(1), samtools-depth(1),

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

15 April 2024 samtools-1.20