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

6       samtools coverage - produces a histogram or table of coverage per chro‐
7       mosome
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SYNOPSIS

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

15       Computes  the  depth  at each position or region and draws an ASCII-art
16       histogram or tabulated text.
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18       The tabulated form uses the following headings.
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21       rname       Reference name / chromosome
22       startpos    Start position
23       endpos      End position (or sequence length)
24       numreads    Number reads aligned to the region (after filtering)
25       covbases    Number of covered bases with depth >= 1
26       coverage    Percentage of covered bases [0..100]
27       meandepth   Mean depth of coverage
28       meanbaseq   Mean baseQ in covered region
29       meanmapq    Mean mapQ of selected reads
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OPTIONS

33       Input options:
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36       -b, --bam-list FILE
37               List of input BAM files, one file per line [null]
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39       -l, --min-read-len INT
40               Ignore reads shorter than INT base pairs [0]
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42       -q, --min-MQ INT
43               Minimum mapping quality for an alignment to be used [0]
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45       -Q, --min-BQ INT
46               Minimum base quality for a base to be considered [0]
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48       --rf, --incl-flags STR|INT
49               Required flags: skip reads with mask bits unset [null]
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51       --ff, --excl-flags STR|INT
52               Filter  flags:  skip  reads  with  mask  bits  set  [UNMAP,SEC‐
53               ONDARY,QCFAIL,DUP]
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55       -d, --depth INT
56               Maximum allowed coverage depth [1000000]. If 0, depth is set to
57               the maximum integer value effectively removing any depth limit.
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60       Output options:
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63       -m, --histogram
64               Show histogram instead of tabular output.
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66       -A, --ascii
67               Show only ASCII characters in histogram using colon  and  full‐
68               stop for full and half height characters.
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70       -o, --output FILE
71               Write output to FILE [stdout].
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73       -H, --no-header
74               Don't print a header in tabular mode.
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76       -w, --n-bins INT
77               Number of bins in histogram.  [terminal width - 40]
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79       -r, --region REG
80               Show specified region. Format: chr:start-end.
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82       -h, --help
83               Shows command help.
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EXAMPLES

87       Running coverage in tabular mode, on a specific region, with tabs shown
88       as spaces for clarity in this man page.
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91         samtools coverage -r chr1:1M-12M input.bam
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93         #rname  startpos  endpos    numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
94         chr1    1000000   12000000  528695    1069995   9.72723   3.50281    34.4       55.8
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97       An example of the histogram output is below, with ASCII  block  charac‐
98       ters replaced by "#" for rendering in this man page.
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101         samtools coverage -A -w 32 -r chr1:1M-12M input.bam
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103         chr1 (249.25Mbp)
104         >  24.19% | .                              | Number of reads: 528695
105         >  21.50% |::                              |     (132000 filtered)
106         >  18.81% |::                              | Covered bases:   1.07Mbp
107         >  16.12% |::                           :  | Percent covered: 9.727%
108         >  13.44% |::  :  .       ::            : :| Mean coverage:   3.5x
109         >  10.75% |:: ::  :       ::          : : :| Mean baseQ:      34.4
110         >   8.06% |:::::  :       ::        : : : :| Mean mapQ:       55.8
111         >   5.37% |::::: ::      :::      : ::::: :|
112         >   2.69% |::::: :::     :::  ::: :::::::::| Histo bin width: 343.8Kbp
113         >   0.00% |:::::::::::. :::::::::::::::::::| Histo max bin:   26.873%
114                 1.00M     4.44M     7.87M       12.00M
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AUTHOR

120       Written by Florian P Breitwieser.
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SEE ALSO

124       samtools(1), samtools-depth(1),
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126       Samtools website: <http://www.htslib.org/>
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130samtools-1.15.1                  7 April 2022             samtools-coverage(1)