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

       Written by Florian P Breitwieser.

       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

       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

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

       Input options:

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

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

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

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

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

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

       -d,--depthINT
               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,--outputFILE
               Write output to FILE [stdout].

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

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

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

       -h,--help
               Shows command help.

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

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

samtools-1.21                                   12 September 2024                           samtools-coverage(1)

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