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

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The new version will be updated and maintained in hewm2008/BamDeal, please click below Link to download the latest version

hewm2008/BamDeal

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-1.12/htslib-1.12 htslib >=1.12  
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

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Parameter description

Program: BamDeal
Version: 0.27   hewm2008@gmail.com      2021-12-02

        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)
	SiteRead	Extract the read (with base) covering the SNP site

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

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• 1. 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>

• 2. 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  ./

• 3. 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>

• 4. 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

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Format Introduction

• sam/bam format
• soap format chinese soap introduction

5) Discussing

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• 📧 hewm2008@gmail.com / hewm2008@qq.com
• join the QQ Group : 125293663

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