PROGRAM: vcfPrinter

DESCRIPTION: Generates multi-sample Variant Call Format (VCF) file from single sample VCF files.

AUTHOR: Uday Evani, Danny Challis, Jin Yu, Fuli Yu

CONTACT: evani@bcm.edu

Date: 30 Dec, 2010
UPDATED: 23 August, 2012

COMPILATION: None needed.

SYSTEM REQUIREMENTS: 

	* Unix-like operation systems
	* Ruby 1.8.5+: http://www.ruby-lang.org/en/downloads/
	* SAMtools must be installed and runnable by invoking the "samtools" command
      -SAMtools may be obtained at http://samtools.sourceforge.net/

	Note: The vcfPrinter has been tested on ruby 1.8.5 and samtools version: 0.1.12a (r862) 

LICENSE: 

This software is free for all uses with the following restrictions:
    * No part of this software, or modifications thereof, may be redistributed for
        any purpose to any other company, person, or individual, without prior written
        permission from the author.
    * This software is provided AS IS. Baylor College of Medicine assumes no
        responsibility or liability for damages of any kind that may result, directly
        or indirectly, from the use of this software.
    * The above copyright notice must be preserved in the executable About dialog or
        made visible to users in some other way.

USAGE: Type "ruby vcfPrinter.rb"  from the command line followed by "--usage" or "-h" to show the command line argument options.

	ruby vcfPrinter.rb 
		-i "<Location of your VCF files>" 
		-o <output file name> 
		-b "<Location of Bam files associated with VCF files> OPTIONAL " 
		-r <Reference fasta file> OPTIONAL 
		-p <Will not merge non-PASS variants, based on the PASS tag in filter field> OPTIONAL
	
	Example command line:
	ruby vcfPrinter.rb -i "/home/user/data/*.vcf" -o /home/user/data/outfile.vcf -b "/home/user/data/*.bam" -r /home/user/ref/human_b36_male.fa
	
	Note: 
		* The VCF and BAM file arguments have to be wrapped in quotes ("). This is because of how glob are executed in Ruby. 
		* The BAM files need to be indexed.
		*The individual sample VCF filenames must follow the convention:
	 [sample_name].vcf and corresponding BAM files should be named [sample_name].bam

Note:
	* Rite now vcfPrinter has been designed only to work with Atlas Indel and Atlas SNP generated VCF files.

	* vcfPrinter requires single sample VCF files in v4.0 format. A description of the format can be found at:
http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0

Changes:
1. Added the -p to filter nonPASS variants
