removing somatic file

sequenceqc_somatic.pl

-#!/usr/bin/perl -w
-#uploadqc.pl
-
-use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);
-my %opt = ();
-my $results = GetOptions (\%opt,'refdir|r=s','input|i=s','output|o=s','help|h');
-
-open MATE, "<$opt{input}" or die $!;
-
-### Begin File Information ###
-my @stats = stat("$opt{input}");
-my ($day,$month,$year) = (localtime($stats[9]))[3,4,5];
-$year += 1900;
-$month++;
-$date = join("-",$year,sprintf("%02s",$month),sprintf("%02s",$day));
-$fileowner = 's'.$stats[4];
-$fileowner = $fileowner;
-### End File Information ###
-
-### Begin Version Information ###
-my $source = `zgrep '#' $opt{refdir}\/cosmic.vcf.gz |grep source`;
-my $cosmic_ref = (split(/=/, $source))[1];
-chomp($cosmic_ref);
-my $dbsnp_source = `zgrep '#' $opt{refdir}\/dbSnp.vcf.gz |grep dbSNP_BUILD_ID`;
-my $dbsnp_ref = (split(/=/, $dbsnp_source))[1];
-chomp($dbsnp_ref);
-my $gen_ref = (split(/\//,$opt{refdir}))[-1];
-my $gittag = `cd /project/PHG/PHG_Clinical/clinseq_workflows;git describe --abbrev=0 --tags`;
-chomp $gittag;
-### End Version Information ###
-
-while (my $line = <MATE>) {
-    chomp($line);
-    my ($sam1,$pf,$sam2,$corr,$depth) = split(/\t/,$line);
-    $sam1 =~ s/\.vcf//g;
-    $sam2 =~ s/\.vcf//g;
-    open OUT, ">$opt{output}" or die $!;
-    my $status= 'PASS';	
-    $status='FAIL' if($pf eq 'unmatched');
-    print OUT join("\n","Sample_1\t".$sam1,"Sample_2\t".$sam2,"Correlation\t".$corr,
-		   "Depth\t".$depth,"Status\t".$status,"Somatic_Date\t".$date,
-		   "File_Owner\t".$fileowner,"Workflow_Version\t".$gittag,
-		   "Cosmic_Reference\t".$cosmic_ref,"dbSnp_Reference\t".$dbsnp_ref,
-		   "Genome_Reference\t".$gen_ref),"\n";
-}
-
-
-