README

Components of the WTSI genotype analysis pipeline.

This pipeline is designed to process large volumes of raw genotyping
data into genotype calls. The platform supported is Illumina Infinium
genotyping microarrays, supplemented with Sequenom genotyping.

Change log is located in: doc/CHANGELOG.md

To install, set the $INSTALL_ROOT environment variable to the path of the
desired installation directory, and run src/bash/install.sh. This installs
the Perl and Ruby components of the pipeline. It recursively installs
non-core Perl dependencies from CPAN, and requires approximately 120 MB of
disk space.

The gender check used as a QC metric is also available as a standalone
application; see below.

Requirements:


Pipeline:

 Ruby 1.8.7
 Percolate              https://github.com/wtsi-npg/Percolate
 Simtools               https://github.com/wtsi-npg/simtools
 Plinktools             https://github.com/wtsi-npg/plinktools
 Bcftools               https://github.com/samtools/bcftools


Install script:
 cpanm >= 1.7042        http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo


QC scripts:

 Simtools >= 2.2	https://github.com/wtsi-npg/simtools
 R >= 2.11.1
 R mixtools library	http://cran.r-project.org/web/packages/mixtools/index.html


Pipeline metadata management:

 Perl >= v5.8.8 
 DBIx::Class            http://search.cpan.org/~arodland/DBIx-Class/
 SQLite                 http://sqlite.org/


Pipeline components:

 Illuminus              https://github.com/wtsi-npg/Illuminus
 Gftools                https://github.com/wtsi-npg/Gftools
 genotype-call          https://github.com/wtsi-npg/genotype-call


Environment variables:

 PATH       Should include path to <install_dir>/bin and to simtools
 PERL5LIB   Should include path to <install_dir>/src/perl/lib/
 R_LIBS     Should include path to mixtools library installation



### Gendermix: standalone gender check ###

The 'Gendermix' gender check method can be installed as a standalone 
application.  See doc/standalone_sexcheck_howto.org for more information.

The standalone check omits much of the pipeline code; it does not require 
Ruby, Percolate, DBIx::Class, SQLite, Illuminus, or genotype-call.  
Other requirements are still in effect.  Gendermix needs the Gftools package 
for I/O of Plink data, as well as R and the mixtools library.  Environment 
variables should be set as described above.