add gt info virmid

variants/addgt_virmid.pl

@@ -17,6 +17,15 @@ while (my $line = <VCF>) {
     }else {
 	my ($chrom, $pos,$id,$ref,$alt,$score,
 	    $filter,$annot) = split(/\t/, $line);
-	print OUT join("\t",$line,'GT','0/0','0/1'),"\n";
+	foreach $a (split(/;/,$annot)) {
+	    my ($key,$val) = split(/=/,$a);
+	    $hash{$key} = $val;
+	}
+	$normalgt=join(":",'0/0',$hash{NDP},$hash{NAC},$hash{NDP}-$hash{NAC},
+		       join(',',$hash{NDP}-$hash{NAC},$hash{NAC}));
+	$tumorgt=join(":",'0/0',$hash{DDP},$hash{DAC},$hash{DDP}-$hash{DAC},
+		       join(',',$hash{DDP}-$hash{DAC},$hash{DAC}));
+	print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,
+		       'GT:DP:AO:RO:AD',$normalgt,$tumorgt),"\n";
     }
 }