samtools-coverage

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	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       12.00M

AUTHOR

Written by Florian P Breitwieser.