得到測序文件進行比對后經常需要對bam文件進行覆蓋深度、靶向捕獲效率的統計分析進行初步質控。
這里介紹一個輸出結果比較多的軟件bamdst，bamdst可以一次性輸出包括深度、覆蓋度、靶向捕獲統計、flanking區域統計在內的多個指標。
Github地址
用起來比較方便，具體使用可以參考github。

安裝：

    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.

其中區域的bed文件可以從測序公司的網站上下載，也可以根據需要自己制作。
自己制作bed可以到UCSC網站