POPBAM
POPBAM is a tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
INTRODUCTION
This is the fourth beta release (0.4b) of the POPBAM program. The source code has primarily been alpha tested on Debian and Red Hat based operating systems using the GNU C++ compiler. A Makefile is provided for the GNU C++ or clang compilers with three compilation modes: release (default), debug, and profile.
OBTAINING THE SOURCE CODE
The POPBAM source code is available to download freely from GitHub at
[http://dgarriga.github.io/POPBAM/]
as either a gzipped tar file or a zipped file with the prefix
dgarriga-POPBAM-<version>
where is the current version number of POPBAM.
The only dependency of the POPBAM program is the zlib compression library and headers. Please insure these are installed on your system before attempting to compile POPBAM.
COMPILING THE SOURCE CODE
Once downloaded, you can extract the popbam/ directory using the command
dgarriga-POPBAM-<version>.tar.gz
or
unzip dgarriga-POPBAM-<version>.zip
Move into the POPBAM source code directory by
cd popbam
Then you can simply type
make
to build the source code. If you have administrator privileges, you can automatically install the POPBAM executable into the /usr/local/bin directory by typing
sudo make install
Lastly, you can clean the POPBAM directory by using
make clean
GETTING HELP USING THE PROGRAM
Currently, the primary resource for helping users run POPBAM is a manpage. If one has system administrator privileges, the popbam.1 file can be installed into the system manpath or, alternatively, the POBPAM manpage can be viewed in the current directory by typing
man ./popbam.1
EXAMPLE DATA SET
To test the build of POPBAM, the user may download an example BAM file from the web site:
[http://kimura.biology.rochester.edu/data/popbam/trial.bam]
This BAM files comprises a single read group each from nine lines of Drosophila melanogaster from sub-Saharan Africa and one line from France. For the outgroup sequence, there is a single Drosophila mauritiana read group. This example contains only reads that map to the X chromosome of the Drosophila melanogaster reference genome (build 5.45).