samtools-coverage - Man Page
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 | 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.
- -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 12.00MAuthor
Written by Florian P Breitwieser.
See Also
samtools(1), samtools-depth(1),
Samtools website: <http://www.htslib.org/>
Referenced By
samtools(1), samtools-depth(1).