vt-bundle/clean_nist_giab_v2.19 at master · atks/vt-bundle · GitHub

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#!/usr/bin/perl -w

use warnings;
use strict;
use POSIX;
use Getopt::Long;
use File::Path;
use File::Basename;
use Pod::Usage;

=head1 NAME

clean_nist_giab_v2.19

=head1 SYNOPSIS

 clean_nist_giab_v2.19 [options]

=head1 DESCRIPTION

 Adds missing INFO meta information in headers.

=cut

#option variables
my $help;
my $verbose;
my $debug;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help, 'v'=>\$verbose, 'd'=>\$debug)
  || scalar(@ARGV)!=1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

my $inputVCFFile = $ARGV[0];

open(VCF, "zcat $inputVCFFile |") || die "Cannot open $inputVCFFile";

while(<VCF>)
{
    chomp;

    if (/^#/)
    {
        if (/^#CHROM/)
        {
			print "##INFO=<ID=PLNCIIonWG,Number=.,Type=String,Description=\"Genotype likelihoods (PL) for ~80x mean 237bp Ion Torrent exome sequencing from Life Technologies, preceded by filtering info if this dataset was not used due to evidence of bias\"\n";
        }

		print "$_\n";
    }
    else
    {
        print "$_\n";
    }
}