sunnycqcn / bamdeal

BamDeal: a comprehensive toolkit for bam manipulation

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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Download
 
Pre-installations of 4 libraries or softs are required before installing BamDel  
1 htslib: samtools-1.6/htslib-1.6  
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]

For linux/Unix and macOS

        tar -zxvf  BamDeal-XXX.tar.gz
        cd BamDeal-XXX;
        ./configure;        
		make;                  
        ./bin/BamDeal

Note: If fail in [./configure], to find library htslib, you can add LDFLAGS to find the htslib library and CPPFLAGS to find the htslib header [ ./configure LDFLAGS=-L/usr/lib/ CPPFLAGS=-I/usr/include/]

2) Features

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Parameter description

Program: BamDeal
Version: 0.19   [email protected]      2018-05-28

        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

statistics

Module	Function	Description
Summary
	Coverage	Calculate Genome Coverage/Depth/GC Dis based Bam
	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

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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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• 📧 [email protected] / [email protected]
• join the QQ Group : 125293663

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