得到測序文件進行比對后經(jīng)常需要對bam文件進行覆蓋深度、靶向捕獲效率的統(tǒng)計分析進行初步質(zhì)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(tǒng)計、flanking區(qū)域統(tǒng)計在內(nèi)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(qū)域的bed文件可以從測序公司的網(wǎng)站上下載，也可以根據(jù)需要自己制作。
自己制作bed可以到UCSC網(wǎng)站
