VCF to calls format

Perl script that reads through a VCF file and prints it out in the "calls" format.

Although i could not find any proper documentation for the calls format, it can be described as diploid genotype calls represented using ambiguous DNA bases for each individual with the first line being the individual id's or names and the following lines being the genotypes at different positions.

 #!/usr/bin/perl  
 use List::Util qw[min max];  
 # Input parameters  
 my $vcf_file = $ARGV[0];  
 #Go through fasta file, extract sequences  
 open(IN, $vcf_file);  
 while($z=<IN>) {  
      if($z=~m/^##/){}  
      elsif($z=~m/^#/){  
           print "scaffold\tposition";  
           chomp $z;  
           @values=split(/\t/,$z);  
           $totind=scalar @values;  
           for($i=9;$i<$totind;$i++){  
           print "\t$values[$i]";  
           }  
      print "\n";  
      }  
      else{  
           chomp $z;  
           @values=split(/\t/,$z);  
           $refbase=$values[3];  
           $altbase=$values[4];  
                if(length $altbase < 2){#skip tri-allelic sites  
                     print "$values[0]\t$values[1]";  
                     $totind=scalar @values;  
                     for($i=9;$i<$totind;$i++){  
                     @parts=split(/\:/,$values[$i]);  
                $parts[0] =~ s/\///g;$parts[0] =~ s/0/$refbase/g;$parts[0] =~ s/1/$altbase/g;  
                $parts[0] =~ s/[A][A]/A/ig;$parts[0] =~ s/[T][T]/T/ig;$parts[0] =~ s/[C][C]/C/ig;$parts[0] =~ s/[G][G]/G/ig;$parts[0] =~ s/[.][.]/N/g;  
                $parts[0] =~ s/[AT][AT]/W/ig;$parts[0] =~ s/[GT][GT]/K/ig;$parts[0] =~ s/[AC][AC]/M/ig;$parts[0] =~ s/[AG][AG]/R/ig;$parts[0] =~ s/[CT][CT]/Y/ig;$parts[0] =~ s/[CG][CG]/S/ig;  
                     print "\t$parts[0]";  
                     }  
           print "\n";  
           }  
      }  
 }#end of file while  
 close IN;  
 #perl vcftocalls.pl genotyped.vcf > genotyped.calls