GATK.remove.hdfilter.pl

#!/usr/bin/perl



=head1 Program Description

    This program is simply designed to filter the SNP and INDEL sites

    that are marked by the GATK Hard Filter algorithm.

    Delection of multi-altenative SNP sites can be chosen.

=head1 Contact & Version

    Author: Shangzhe Zhang, shangzhezhang@gmail.com

    Date: 2019.2.5

    Version: None

=head1 Command-line Option

    --input <str> Input VCF format file, MUST be gziped;

    --output <str> Output VCF format file, will be gziped by default;

    --multi Set this option if you want to delete the multi-alt SNPs (DON'T use when --type INDEL)

    --marker The marker you used in the Hard Filter Process, e.g. my_snp_filter

    --type <str> Set the variant type: SNP or INDEL;

    --help Show this help text

=head1 Usage Example

    remove.hdfilter.pl --input IN.vcf.gz --output OUT.vcf.gz --type SNP --marker my_snp_filter --multi

=cut



use strict;
use warnings;
use Getopt::Long;
my ($infile, $outfile, $multi, $marker, $type, $help);

GetOptions(
           "input:s" =>\$infile,
           "output:s" =>\$outfile,
           "multi"=>\$multi,
           "help"=>\$help,
           "type:s"=>\$type,
           "marker:s" =>\$marker
          );

die `pod2text $0` if ($help || ! $marker);
undef($multi) if ($type eq "INDEL");

#die `pod2text $0` if ($infile !~ /.*\.gz$/);

if ($outfile !~ /.*\.gz$/){
    $outfile = $outfile.".gz";
}

open OUT, "| gzip - > $outfile";
open IN, " zcat $infile | ";
while(<IN>){
    chomp;
    if (/^#/){
        print OUT "$_\n";
        next;
    }
    my @a = split/\s+/;
    next if ($a[6] eq $marker);
    if ($multi){
        next if ($a[4] =~ /,/);
    }
    print OUT "$_\n";
}
close IN;
close OUT;