annot_sv.pl

#!/usr/bin/perl -w
#svvcf2bed.pl

use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);

my %opt = ();
my $results = GetOptions (\%opt,'input|i=s','refdb|r=s','help|h');

my $vcf = $opt{input};

my %lines;
my %eventid;
my $ct = 0;
open IN, "<$vcf" or die $!;
while (my $line = <IN>) {
  chomp($line);
  if ($line =~ m/^#CHROM/) {
    my @header = split(/\t/,$line);
    ($chrom, $pos,$id,$ref,$alt,$score,
     $filter,$info,$format,@subjacc) = split(/\t/, $line);
  }
  next if $line =~ m/#/;
  my ($chrom, $pos,$id,$ref,$alt,$score,
      $filter,$annot,$format,@gts) = split(/\t/, $line);
  $ct ++;
  my %hash = ();
  foreach $a (split(/;/,$annot)) {
    my ($key,$val) = split(/=/,$a);
    $hash{$key} = $val unless ($hash{$key});
  }
  if ($id eq 'N') {
      $id = 'NB'.sprintf("%06s",$ct);
  }
  my $evid = (split(/_/,$id))[0];
  $hash{'END'} = $pos+1 unless $hash{'END'};
  @deschead = split(":",$format);
 F1:foreach $sample (@subjacc) {
    my $allele_info = shift @gts;
    @ainfo = split(/:/, $allele_info);
    my %gtinfo = ();
    foreach $k (0..$#deschead) {
      $gtinfo{$deschead[$k]} = $ainfo[$k];
    }
    unless ($gtinfo{SU}) {
	$gtinfo{SU} = 0;
	$gtinfo{SU} = $gtinfo{RV}+$gtinfo{DV} if ($gtinfo{RV} && $gtinfo{DV});
    }
    $gtinfo{CN} = '' unless  $gtinfo{CN};
    if ($alt =~ m/chr(\w+):(\d+)/i) {
	if ($1 eq $chrom) {
	    my $locus = join(":",$chrom,$pos,$2);
	    $eventid{$id} = $locus;
	    $lines{$evid}{$locus}{$sample} =  join("\t",$hash{SVTYPE},$gtinfo{CN},$gtinfo{SU});
	}elsif ($id =~ m/_\d+/) {
	    my $locus = join(":",$chrom,$pos,$hash{END});
	    $eventid{$id} = $locus;
	    $lines{$evid}{$locus}{$sample} =  join("\t",$hash{SVTYPE},$gtinfo{CN},$gtinfo{SU});
	}else {
	    my $locus1 = join(":",$chrom,$pos,$hash{END});
	    my $id1 = $id."_1";
	    $eventid{$id1} = $locus1;
	    my $locus2 = join(":",'chr'.$1,$2,$2+1);
	    my $id2 = $id."_2";
	    $eventid{$id2} = $locus2;
	    $lines{$evid}{$locus1}{$sample} =  join("\t",$hash{SVTYPE},$gtinfo{CN},$gtinfo{SU});
	    $lines{$evid}{$locus2}{$sample} =  join("\t",$hash{SVTYPE},$gtinfo{CN},$gtinfo{SU});
	}
    }else {
	if ($hash{CHR2} && $hash{CHR2} eq $chrom) {
	    my $locus = join(":",$chrom,$pos,$hash{END});