[sambamba depth] documentation

NAME

sambamba-depth - depth statistics for BAM data

SYNOPSIS

sambamba-depth region|window|base [options] input.bam [input2.bam [...]]

DESCRIPTION

sambamba-depth requires bams to be coordinate-sorted and indexed.

The tool has three modes: base, region, and window, each name means per which unit to print the statistics.

OPTIONS

-F, --filter=FILTER

set custom filter for alignments; the default value is 'mapping_quality > 0 and not duplicate and not failed_quality_control'

-o, --output-file=FILENAME

output filename (by default /dev/stdout)

-t, --nthreads=NTHREADS

maximum number of threads to use

-c, --min-coverage=MINCOVERAGE

minimum mean coverage for output (default: 0 for region/window, 1 for base)

-C, --max-coverage=MAXCOVERAGE

maximum mean coverage for output

-q, --min-base-quality=QUAL

don't count bases with lower base quality

--combined

output combined statistics for all samples

-a, --annotate

add additional column of y/n instead of skipping records not satisfying the criteria

-m, --fix-mate-overlaps

detect overlaps of mate reads and handle them on per-base basis

EXAMPLES

Get average depth in bam per bed region

$ sambamba-depth region -L example.bed example.bam

Will output something like this:

# chrom chromStart      chromEnd        readCount       meanCoverage    sampleName
chr1    157869455       158026560       27562   23.6111 sample1
...
chr22   8901514 9101488 48617   32.9561 sample1