BamDeal
BamDeal: a comprehensive toolkit for bam manipulation
BamDeal is a full-featured toolkit for comprehensive analysis of bam file,
BamDeal is implemented in C/C++ language, available for Linux and Mac OS X operating system.
1) Download and Install
Download
For linux/Unix static
you can use the statically compiled programs directly
chmod 755 ./bin/BamDeal_Linux ./bin/BamDeal_Linux # mv BamDeal_Linux BamDeal
For linux/Unix and macOS compile
Pre-installations of 4 libraries or softs are required before installing BamDeal
1 htslib: samtools-1.9/htslib-1.9 1.5 <= htslib <= 1.9
2 g++ : g++ with --std=c++11 > 4.8+ is recommended
3 zlib : zlib > 1.2.3 is recommended
4 R : R with ggplot is recommended
- To compile BamDeal, do [ ./configure] first, then [make]
- Final software can be found in the direcoty [bin/BamDeal]
tar -zxvf BamDeal-XXX.tar.gz cd BamDeal-XXX; chmod 755 configure; ./configure make; mv BamDeal bin/; ./bin/BamDeal
Note1: If fail in [./configure], to find library htslib, you can add LDFLAGS to find the htslib library and CXXFLAGS and CFLAGS to find the htslib header [ ./configure LDFLAGS=-L/usr/lib/ CXXFLAGS=-I/usr/include/ CFLAGS=-I/usr/include/];
export 'LIBRARY/CFLAGS/CXXFLAGS' environment variables to set the htslib path also can be a way to compile, such : export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH;
Note2: you can use the statically compiled programs directly [chmod 755 ./bin/BamDeal_Linux; ./bin/BamDeal_Linux]
2) Features
Parameter description
Program: BamDeal
Version: 0.23 hewm2008@gmail.com 2019-05-24
Usage:
convert convert tools
modify modify tools
statistics statistics analysis tools
visualize visualize tools for bam
Help Show help in detail
convert
Module | Function | Description |
---|---|---|
Summary | ||
soap2bam | soap --> bam/sam Format | |
bam2soap | bam/sam --> soap Format | |
bam2fq | bam/sam --> Fastq Format | |
bam2fa | bam/sam --> Fasta Format |
modify
Module | Function | Description |
---|---|---|
Summary | ||
bamFilter | filter low quality read in bam | |
bamSplit | split single/muti-Bam by chr | |
bamAssign | split single/muti-Bam by assign chr | |
bamCat | Merge/Cat diff header muti bam to one bam | |
bamRand | random out partly of bam read | |
bamSubChr | get/remove some chr form bam | |
bamShiftQ | modify seq phred quality in bam | |
bamLimit | Limit big bam to muti subbam by fix line |
statistics
Module | Function | Description |
---|---|---|
Summary | ||
Coverage | Calculate Genome Coverage/Depth/GC Dis based Bam (v1.32) | |
BasesCount | Calculate Genome every Site's four base Depth | |
DeteCNV | Detect CNV/Deletion Region by merge Depth info based Bam | |
DeteSV | Detect SV by Pair End Read insert size in Bam | |
LowDepth | GiveOut bed file of low Depth Region(may BigDeletion) |
visualize
Module | Function | Description |
---|---|---|
Summary | ||
StatQC | Basic Stat and qualty control,Show gc-depth... result Fig | |
DepthCov | Show pdf Fig of Depth Dis & Depth~Coverage | |
DepthGC | Show pdf Fig of Depth~RefGC | |
DepthSlide | Show Manhattan Fig of Depth sliding Windows along genome |
3) Examples
-
- convert
#convert soap 2 bam
./bin/BamDeal convert soap2bam -InSoap <in.soap> -OutBam <out.bam> -Dict Ref.fa
#convert bam 2 soap
./BamDeal convert bam2soap -InFile <in.bam> -OutPut <Out.soap>
-
- modify
# cat diff header bam to one bam
./BamDeal modify bamCat -InFile A.bam -InFile B.bam -OutFile C.bam
# merge muti sort bam to an sort bam
./BamDeal modify bamCat -InList <bam.Sort.list> -OutFile <out.sort.bam> -Merge
# split bam by chr
./BamDeal modify bamSplit -InList <bam.list> -ReSetHead -OutDir ./
-
- statistics
# detect CNV/Deletion Region based bam file
./BamDeal statistics DeteCNV -List <bam.list> -OutPut <outPrefix>
# stat coverage and depth each chr
./BamDeal statistics Coverage -List <bam.list> -OutPut <out> -Ref Ref.fa -Stat
# GiveOut bed file of low Depth Region
./BamDeal statistics LowDepth -InList <bam.list> -OutPut <out.bed>
-
- statistics
# Show Manhattan Fig of Depth sliding Windows along genome
./BamDeal visualize DepthSlide -InList <bam.list> -Ref <Ref.fa> -OutPut <outPrefix>
# Show pdf Fig of Depth~RefGC
./BamDeal visualize DepthGC -InList <bam.list> -Ref <Ref.fa> -OutPut <outPrefix>
# Show pdf Fig of Depth Dis & Depth~Coverage
./BamDeal visualize DepthCov -InList <bam.list> -OutPut <outPrefix>
see more other Usage in the Documentation
4) Format
Format Introduction
5) Discussing
📧 hewm2008@gmail.com / hewm2008@qq.com- join the QQ Group : 125293663
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