The Platypus variant caller. To build Platypus, do the following:
Then to run do
python bin/Platypus.py --bamFiles=BAM.bam --refFile=REF.fa --output=variants.vcf
Platypus has been tested with Python 2.6 and 2.7, and requires Cython 0.20.2 or later
PREREQUISITES: Platypus requires htslib 1.2.1 or greater. htslib can be downloaded from the htslib website http://www.htslib.org/download/.
To build and install htslib, cd into htslib source and type 'make install'. This will install htslib under /usr/local/ (see note below). To install htslib in any other directory use 'make install prefix=/path/to/dir'.
NOTE: htslib should be installed in a standard location (e.g. /usr/local/). If not installed in a standard location, you will need to set your library paths:
export C_INCLUDE_PATH=/path/to/dir/include export LIBRARY_PATH=/path/to/dir/lib (only for making) export LD_LIBRARY_PATH=/path/to/dir/lib
Note the '/include' and '/lib' sub-directories. e.g. if you installed htslib under /Users/me/htslib then set
export C_INCLUDE_PATH=/Users/me/htslib/include export LIBRARY_PATH=/Users/me/htslib/lib export LD_LIBRARY_PATH=/Users/me/htslib/lib
htslib will automatically make the 'include' and 'lib' directories on install.
export C_INCLUDE_PATH=/path/to/dir/include export LIBRARY_PATH=/path/to/dir/lib (only for making) export DYLD_FALLBACK_LIBRARY_PATH=/path/to/dir/lib