11    608502 
11    1016988 
11    1017495 
11    1018088 
11    3661585
##</code><code>##

#!/usr/bin/perl
use warnings;
use strict;
use v5.10;

#  Create program to read in a series of VCF files, outputting a two-column
#  file consisting of chromosome and coordinate for each site seen in one or
#  more files ('master-site-list').

die "Give the names of each VCF" if @ARGV < 1;

my $number_of_files = @ARGV;
my $infile;
my $current_file_number = 0;

my %hash_of_chroms;

open my $outfile, '>', "master-site-list" or die "Cannot open output file: $!";

until ( $current_file_number >= $number_of_files ) {

    open $infile, '<', $ARGV[$current_file_number]
      or die "Cannot open VCF file: $!";

    while (<$infile>) {
        chomp;
        next if /^#/;

        my ( $chr, $coord ) = split(/\s+/);

        push @{ $hash_of_chroms{$chr} }, $coord
          unless defined $hash_of_chroms{$chr}[$coord];   # don't add duplicates
    }

    $current_file_number++;

    close $infile;

}

my %sorted_hash_of_chroms;
foreach my $chrom ( keys %hash_of_chroms ) {
    push @{ $sorted_hash_of_chroms{$chrom} },
      sort { $hash_of_chroms{$a}->[0] <=> $hash_of_chroms{$b}->[0] }
      keys %hash_of_chroms;
}

foreach my $chrom ( keys %hash_of_chroms ) {
    say $outfile "$chrom\t@{ $hash_of_chroms{$chrom} }";
}

close $outfile;

##</code><code>##

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RR,Number=1,Type=Integer,Description="Reference Read Depth">
##FORMAT=<ID=VR,Number=.,Type=Integer,Description="Variant Read Depth(s)">
##FORMAT=<ID=PL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=SF,Number=.,Type=String,Description="Source file(s)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA19238
1	874816	.	C	CT	10	FINAL_AMBG	SF=bcm_illum,bi_illum;validation_ratio=52/1019;sets=bcm_illum,bi_illum;samples=NA19238	GT	1/0
1	1647893	.	C	CTTTCTT	30	FINAL_NOT_CONFIRMED	SF=bcm_illum,bcm_solid;validation_ratio=0/3380;sets=bcm_illum,bcm_solid;samples=NA19238	GT	0/0
1	7889972	rs57875989	GAGAATCCATCCCATCCTACTGCCAGCGCTCTGTCCACAGGATCGCCTCCCATGA	G	33190	DESIGN_FAIL	SF=bi_illum	GT	./.
1	14106394	.	A	ACTC	100	FINAL_CONFIRMED	SF=bcm_illum,bcm_solid,bc_illum;validation_ratio=864/1754;sets=bcm_illum,bcm_solid,bc_illum;samples=NA19238	GT	1/0