得到测序文件进行比对后经常需要对bam文件进行覆盖深度、靶向捕获效率的统计分析进行初步质控。
这里介绍一个输出结果比较多的软件bamdst，bamdst可以一次性输出包括深度、覆盖度、靶向捕获统计、flanking区域统计在内的多个指标。
Github地址
用起来比较方便，具体使用可以参考github。
安装：
git clone https://github.com/shiquan/bamdst
cd bamdst/
make
使用：
bamdst -p <probe.bed> -o ./ in1.bam
PARAMETERS
-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]
OPTIONAL PARAMETERS
-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 (an invalid parament since v1.0.0 )
Use rmdup depth instead of cover depth to calculate the coverage of target regions and
so on.
其中区域的bed文件可以从测序公司的网站上下载，也可以根据需要自己制作。
自己制作bed可以到UCSC网站
