jammy (1) samtools-coverage.1.gz

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 depth at each position or region and draws an ASCII-art histogram or tabulated text.

       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    Proportion of covered bases [0..1]
       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.

       -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

AUTHOR

       Written by Florian P Breitwieser.

SEE ALSO

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

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