| samtools-coverage(1) | Bioinformatics tools | samtools-coverage(1) |
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 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 |
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.
- -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, --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
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
AUTHOR¶
Written by Florian P Breitwieser.
SEE ALSO¶
samtools(1), samtools-depth(1),
Samtools website: <http://www.htslib.org/>
| 12 December 2023 | samtools-1.19 |