paulmenzel / platypus

Platypus Variant Caller

The Platypus variant caller. To build Platypus, do the following:

make

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 to build.

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:

For linux:

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.

For OSX:

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