Bamdst is a lightweight tool to stat the depth coverage of target regions of bam file(s).
Bam file(s) should be properly sorted, and the probe file (bed file) and the output dir
must be specified in the first place.
Normal:
bamdst -p <probe.bed> -o ./ in1.bam
Pipeline mode:
samtools view in1.bam -u | bamdst -p x.bed -o ./ -
-o / --outdir [dir]
set the output dir [mandatory]
-p / --bed [file]
the probe or captured target region file, these regions will be merged first [mandatory]
-f / --flank [num]
if you want calculate the coverage of flank region, set this value, default is 200
--maxdepth [num]
for some projects, the depths of sepcial region are very high, if you don't want show
these unnormal depths in cumulation distrbution file, set the cutoff value to filter them.
default is 0 (no filter).
--cutoffdepth [num]
for some projects, people care about the coverage of specified depth, like 10000x etc.
bamdst just calculate the coverage of 0x, 4x, 10x, 30x, 100x, so you can set this value
to show the specified coverage in the coverage.report file. Default is 0.
--isize [num]
for bad mapped paired reads, the inferred insert size is very huge. So set a cutoff
value for reasonal visual purpose. Default is 2000.
--uncover [num]
set this cutoff value for calculate the bad covered region. Default is <5.
--use_rmdup
Use rmdup depth instead of cover depth to calculate the coverage of target regions and
so on.
Seven files will be created in the output direction. There are:
-coverage.report
-cumu.plot
-insert.plot
-chromosome.report
-region.tsv.gz
-depth.tsv.gz
-uncover.bed
coverage.report
This file contains all the coverage information of target and
flank region, and reads stat information of the input file(s).
cumu.plot
Depth distrbution for plot.
insert.plot
Inferred insert size distribution for plot.
chromosome.report
Depth and coverage information of each chromosome.
region.tsv.gz
For each region in probe file (in.bed), average depth, median
depth and coverage of these regions will be listed in the file.
depth.tsv.gz
For each position in the probe file(in.bed), three kinds depth
value will be calculated, including raw depth, rmdup depth and
the coverage depth. The raw depth is retrieved from input bam
file(s) without any restriction. And the rmdup depth is
calculated after remove duplicated reads and secondary alignment
reads and low map quality reads(mapQ < 20), this value is similar
with the output depth of samtools depth. The coverage depth is
the raw depth with consider of deletion region, so this value
should be equal to or greated than the raw depth. We usw raw depth
to stat the coverage information in the coverage.report file. If
you want use rmdup depth to calculate the coverage, please use
the parameter "--use_rmdup".
uncover.bed
This bed file contains the bad covered or uncovered region in the
input bam file(s) against the probe file. Set the cutoff value of
uncover by parameter "--uncover"
For a large region, like whole genome region, bamdst may go crash with a segmental fault. I have noticed issues like this, and this bug can be tolerated by split a large region into several small pieces. However, this bug may not be fixed until next major update.