<commit_before>############################
#                          #
# Variant Effect Predictor #
#                          #
############################

Copyright (c) 1999-2011 The European Bioinformatics Institute and
Genome Research Limited.  All rights reserved.

This software is distributed under a modified Apache license.
For license details, please see

http://www.ensembl.org/info/about/code_licence.html

Please email comments or questions to the public Ensembl
developers list at <<EMAIL>>.

Questions may also be sent to the Ensembl help desk at
<<EMAIL>>
  
  

0.0 What's new
==============

Version 2.0 of the Variant Effect Predictor script (VEP) constitutes a complete
overhaul of both the script and the API behind it. It requires at least version
62 of the Ensembl API to function. Here follows a summary of the changes:

- support for SIFT, PolyPhen and Condel non-synonymous predictions in human

- per-allele and compound consequence types

- support for Sequence Ontology (SO) and NCBI consequence terms

- modified output format
  - support for new output fields in Extra column
  - header section containing information on database and software versions
  - codon change shown in output
  - CDS position shown in output
  - option to output Ensembl protein identifiers
  - option to output HGVS nomenclature for variants
  
- support for gzipped input files
  
- enhanced configuration options, including the ability to read configuration
  from a file

- verbose output now much more useful

- whole-genome mode now more stable

- finding existing co-located variations now ~5x faster



1.0 Requirements
================

Version 2.0 of the script requires at least version 62 of the Ensembl Core and
Variation APIs and their relevant dependencies to be installed. See
http://www.ensembl.org/info/docs/api/index.html for details. No explicit
installation of the script is required.



2.0 Introduction
================

Given a set of variant positions and alleles, it is often useful to know how
these variants may affect transcripts and other genetic factors. Ensembl
provides such annotation for the variants stored in its Ensembl Variation
database; using this script it is possible to do the same for novel variants.



3.0 Running the script
======================

The script is run on the command line as follows:

perl variant_effect_predictor.pl [options]

where [options] represent a set of flags and options to the script. These can be
listed using the flag --help:

perl variant_effect_predictor.pl --help

By default the script connects to the public Ensembl database server at
ensembldb.ensembl.org; other connection options are available.


3.1 Basic options
-----------------

--help : display help message and quit

-v (--verbose) : Output status messages as the script runs. Not used by default

-q (--quiet) : Suppress status and warning messages. Not used by default

-c (--config) : Load configuration options from a config file. The config file
should consist of whitespace-separated pairs of option names and settings e.g.:

output_file   my_output.txt
species       mus_musculus
format        vcf
whole_genome  1

This is useful if you find yourself using the same configuration options each
time. You can create a quick version file of this by setting the flags as normal
and running the script in verbose (-v) mode. This will output lines that can be
copied to a config file that can be loaded in on the next run using -c. Note
that any options specified in the normal way overwrite those in the config file.
Not used by default


3.2 Input options
-----------------

-s (--species) : species for your data. This can be the latin name e.g.
"homo_sapiens" or any Ensembl alias e.g. "mouse". Specifying the latin name can
speed up initial database connection as the registry does not have to load all
available database aliases on the server. Default = "human"

-i (--input_file) : input file name. If not specified, the script will attempt
to read from STDIN.

--format : input file format. By default, the script auto-detects the input
file format. Using this option you can force the script to read the input
file as VCF or pileup format. Not used by default.
 
-o (--output_file) : output file name. Default = "variant_effect_output.txt"


3.3 Database options
--------------------

-d (--db_host) : manually define the database host to connect to.
Default = "ensembldb.ensembl.org"

-u (--user) : manually define the database username used when connecting to the
database host. Default = "anonymous"

-p (--password) : manually define the database password used when connecting to
the database host. Not used by default

-r (--registry_file) : defining a registry file (see 4.3 below) overwrites other
connection settings and uses those found in the specified registry file to
connect.
  
-g (--genomes) : override the default connection settings with those for the
Ensembl Genomes public MySQL server. Required when using any of the Ensembl
Genomes species. Not used by default

--db_version [version]: force the script to connect to a specific version of the
Ensembl databases. Not recommended as there will usually be conflicts between
software and database versions. Not used by default


3.4 Output options
------------------

-t (--terms) [ensembl|so|ncbi] : the type of consequence terms to output. The<commit_msg>Minor edits<commit_after>############################
#                          #
# Variant Effect Predictor #
#                          #
############################

Copyright (c) 1999-2011 The European Bioinformatics Institute and
Genome Research Limited.  All rights reserved.

This software is distributed under a modified Apache license.
For license details, please see

http://www.ensembl.org/info/about/code_licence.html

Please email comments or questions to the public Ensembl
developers list at <<EMAIL>>.

Questions may also be sent to the Ensembl help desk at
<<EMAIL>>
  
  

0.0 What's new
==============

Version 2.0 of the Variant Effect Predictor script (VEP) constitutes a complete
overhaul of both the script and the API behind it. It requires at least version
62 of the Ensembl API to function. Here follows a summary of the changes:

- support for SIFT, PolyPhen and Condel non-synonymous predictions in human

- per-allele and compound consequence types

- support for Sequence Ontology (SO) and NCBI consequence terms

- modified output format
  - support for new output fields in Extra column
  - header section containing information on database and software versions
  - codon change shown in output
  - CDS position shown in output
  - option to output Ensembl protein identifiers
  - option to output HGVS nomenclature for variants
  
- support for gzipped input files
  
- enhanced configuration options, including the ability to read configuration
  from a file

- verbose output now much more useful

- whole-genome mode now more stable

- finding existing co-located variations now ~5x faster



1.0 Requirements
================

Version 2.0 of the script requires at least version 62 of the Ensembl Core and
Variation APIs and their relevant dependencies to be installed. See
http://www.ensembl.org/info/docs/api/index.html for details. No explicit
installation of the script is required.



2.0 Introduction
================

Given a set of variant positions and alleles, it is often useful to know how
these variants may affect transcripts and other genetic factors. Ensembl
provides such annotation for the variants stored in its Ensembl Variation
database; using this script it is possible to do the same for novel variants.



3.0 Running the script
======================

The script is run on the command line as follows:

perl variant_effect_predictor.pl [options]

where [options] represent a set of flags and options to the script. These can be
listed using the flag --help:

perl variant_effect_predictor.pl --help

By default the script connects to the public Ensembl database server at
ensembldb.ensembl.org; other connection options are available.


3.1 Basic options
-----------------

--help : display help message and quit

-v (--verbose) : Output status messages as the script runs. Not used by default

-q (--quiet) : Suppress status and warning messages. Not used by default

-c (--config) : Load configuration options from a config file. The config file
should consist of whitespace-separated pairs of option names and settings e.g.:

output_file   my_output.txt
species       mus_musculus
format        vcf
whole_genome  1

This is useful if you find yourself using the same configuration options each
time. You can create a quick version file of this by setting the flags as normal
and running the script in verbose (-v) mode. This will output lines that can be
copied to a config file that can be loaded in on the next run using -c. Note
that any options specified in the normal way overwrite those in the config file.
Not used by default


3.2 Input options
-----------------

-s (--species) : species for your data. This can be the latin name e.g.
"homo_sapiens" or any Ensembl alias e.g. "mouse". Specifying the latin name can
speed up initial database connection as the registry does not have to load all
available database aliases on the server. Default = "human"

-i (--input_file) : input file name. If not specified, the script will attempt
to read from STDIN.

--format : input file format. By default, the script auto-detects the input
file format. Using this option you can force the script to read the input
file as VCF or pileup format. Not used by default.
 
-o (--output_file) : output file name. Default = "variant_effect_output.txt"


3.3 Database options
--------------------

-d (--db_host) : manually define the database host to connect to.
Default = "ensembldb.ensembl.org"

-u (--user) : manually define the database username used when connecting to the
database host. Default = "anonymous"

-p (--password) : manually define the database password used when connecting to
the database host. Not used by default

-r (--registry) : defining a registry file (see 4.3 below) overwrites other
connection settings and uses those found in the specified registry file to
connect.
  
-g (--genomes) : override the default connection settings with those for the
Ensembl Genomes public MySQL server. Required when using any of the Ensembl
Genomes species. Not used by default

--db_version [version]: force the script to connect to a specific version of the
Ensembl databases. Not recommended as there will usually be conflicts between
software and database versions. Not used by default


3.4 Output options
------------------

-t (--terms) [ensembl|so|ncbi] : the type of consequence terms to output. The
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