samtools is a handy tool for sequence alignment and mapping (http://samtools.sourceforge.net/
For more information, please refer to the original article here:
- Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
To get it to work on mac, I’ve decided to compile it.
First, get the sourcecode from http://sourceforge.net/projects/samtools/files/samtools/
Then, decompress the files in ~/bin
Compile it as usual
./configure make make install
You might need to have administrative right to write to system folder as well.
Next, we'll need to add a path to ~/.bash_profile
Include this in ~/.bash_profile to point to SAMTOOLS_HOME
export SAMTOOLS_HOME=~/bin/samtools-0.1.19 export PATH=$SAMTOOLS_HOME:$PATH export PATH=$SAMTOOLS_HOME/bcftools/:$PATH export PATH=$SAMTOOLS_HOME/misc/:$PATH
Now, samtools should be ready for you to use.