Installation and use of BWA and Samtools under Linux

installation process for BWA
The installation of the software requires the following two software installation tasks:
1) BWA
2) Samtools

Installation of 1.BWA
A. Download BWA (download from BWA Source Forge)

Http://bio-bwa.sourceforge.net/bwa.shtml
B. Installing BWA
$ TAR-JXVF bwa-*.tar.bz2
C. Compiling BWA
$ make

Installation of 2.Samtools
A. Download Samtools (download from Samtools Source Forge)

Http://samtools.sourceforge.net/samtools.shtml
B. Installing Samtools
$ TAR-JXVF samtools-*.tar.bz2
C. Compiling Samtools
$ make


BWA Flow of Use
1. Create Index
Create Index File According to reference genome data (e.g. REFERENCE.FA)
$ BWA index-a BWTSW HUMAN_HG18_REF.FA (Human reference genome 19)
2. Mapping the Reads
If it is pair-end data (LEFTREAD.FASTQ and RIGHTREAD.FASTQ) two files are processed separately
$ BWA AlN Reference.fa LEFTREAD.FASTQ Leftread.sai
$ BWA AlN Reference.fa RIGHTREAD.FASTQ Rightread.sai
If the data is Single-end, the
$ BWA AlN Reference.fa SINGLEREAD.FASTQ Singleread.sai
3. Process the mapping output file *.sai into *.sam
If it's pair-end data
$ BWA sampe-f pair-end.sam reference.fa leftread.sai rightread.sai leftread.fastq RIGHTREAD.FASTQ
If it's single-end data
$ BWA samse-f single.sam reference.fa Single.sai SINGLE.FASTQ

REF:

Http://www.cnblogs.com/emanlee/p/4316581.html

Http://www.cnblogs.com/emanlee/p/4316587.html

Http://www.plob.org/2014/01/26/7112.html

Http://www.nikest.com/web/free/2014/1014/93144.html

Installation and use of BWA and Samtools under Linux