wtsi-hgi/Platypus

Name: Platypus

Owner: Wellcome Trust Sanger Institute - Human Genetics Informatics

Description: Platypus Variant Caller

Forked from: andyrimmer/Platypus

Created: 2015-06-10 12:18:18.0

Updated: 2015-06-10 12:18:19.0

Pushed: 2015-06-24 16:22:52.0

Homepage: null

Size: 56034

Language: Python

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README

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