liupfskygre / BamSplit

A efficient software tools to split Bam form all chromosome together to each chr one bam

BamSplit

BamSplit: A efficient software tools to split Bam form all chromosome together to each chr one bam

The newest version of this funtion was integrated into toolkit BamDeal ,please replace BamSplit by this BamDeal.

           ./BamDeal  modify  bamSplit

1. Install

---

Please replace BamSplit with this toolkit BamDeal.

 This software rely htslib，so should Pre-install htslib first samtools-1.5/htslib-1.5
Then Just [make] or [sh make.sh ] to compile this software.
the final software can be found in the Dir [bin/BamSplit]

For linux /Unix and macOS

        tar -zxvf  BamSplit-XXX.tar.gz
        cd BamSplit-XXX;                             # if Link do not work ,Try re-install  two  library
        cd src;                                      #【zlib and htslib】 and copy them to the  library Dir
        make ; make clean                            # BamSplit-XX/src/include/zlib 
        ../bin/BamSplit                              # BamSplit-XX/src/include/gzstream

2. Example

---

• 1. Calculate bam files

#To Calculate bam
	./bin/BamSplit  -List  bam.list 
#Remain all read with -MinQ  -1 
	./bin/BamSplit  -List  bam.list  -OutDir  ./  -MinQ -1
#Remain The same header with all chr
	./bin/BamSplit  -List  bam.list -SameHead 

• 2. Calculate sam files

# To cCalculate sam
	./bin/BamSplit  -List  sam.list  -OutDir  ./  -SameHead 
# Also you the  add the  -MinQ to filter some reads
	./bin/BamSplit  -List  sam.list  -OutDir  ./   -OutSam 

3. Introduction

---

• Parameter description

/BamDeal  modify  bamSplit

        Usage: bamSplit  -InList  <bam.list>  -ReSetHead
        Usage: bamSplit  -InFile A.bam  B.bam

                -InFile    <str>     Input Bam/Sam File to split by chr
                -InList    <str>     Input Bam/Sam File List

                -OutDir    <str>     OutPut Dir for split [./]
                -MinQ      <int>     classify low mapQ<X read to unmap.bam[10]
                -OutSam              OutPut sam.gz File, not [bam]
                -ReSetHead           Reset Out.bam Header only with it's chr

                -help                Show this help [hewm2008 v1.02]

4. Results

---

Format Introduction

• sam bam format

5）Discussing

• email: [e-mail] / [e-mail]
• join the QQ Group : 125293663

######################swimming in the sky and flying in the sea ########################### ##