diff --git a/bin/svParser.pm b/bin/svParser.pm
index 2a9d14f..a332baa 100755
--- a/bin/svParser.pm
+++ b/bin/svParser.pm
@@ -272,8 +272,17 @@ sub lumpy {
     }
   }
 
-  if ( $filter_flags{'s'} ){
-    $filters = somatic_filter( $id, $tumour, $control, $normals, $filters, \%PON_info );
+  if ( $filter_flags{'st'} ){
+    $filters = genotype_filter( $id, $genotype, $filters, 'somatic_tumour' );
+  }
+  elsif ( $filter_flags{'sn'} ){
+    $filters = genotype_filter( $id, $genotype, $filters, 'somatic_normal' );
+  }
+  elsif ( $filter_flags{'gp'} ){
+    $filters = genotype_filter( $id, $genotype, $filters, 'germline_private' );
+  }
+  elsif ( $filter_flags{'gr'} ){
+    $filters = genotype_filter( $id, $genotype, $filters, 'germline_recurrent' );
   }
 
   my @samples = @{ $samples };
@@ -356,7 +365,7 @@ sub lumpy {
 
   my @filter_reasons = @{ $filters };
 
-    ### This might be useless - isn't this happening in somatic_filter() ?
+    ### This might be useless - isn't this happening in genotype_filter() ?
     if (@samples > 1){ # In case there are no control samples...
       # for precise variants:
       if ($info_block !~ /IMPRECISE;/) {
@@ -621,8 +630,8 @@ sub delly {
     $PON_info{$normal} = [ ($sample_info{$id}{$normal}{'DV'} + $sample_info{$id}{$normal}{'RV'}) , $sample_info{$id}{$normal}{'GT'} ];
   }
 
-  if ( $filter_flags{'s'} ){
-    $filters = somatic_filter( $id, $tumour_name, $control_name, $normals, $filters, \%PON_info );
+  if ( $filter_flags{'st'} ){
+    $filters = genotype_filter( $id, $genotype, $filters, 'somatic_tumour' );
   }
 
   if ( $filter_flags{'su'} ){
@@ -642,20 +651,14 @@ sub delly {
 
 sub summarise_variants {
   my ( $SVs, $filter_switch, $region ) = @_;
-
   my ($dels, $dups, $trans, $invs, $filtered) = (0,0,0,0,0);
   my ($tds, $CNVs, $ins) = (0,0,0);
 
   my ( $chromosome, $query_start, $query_stop, $specified_region) = parseChrom($region) if $region;
-
   my %support_by_chrom;
-
   my $read_support;
-
   my %filtered_sv;
-
   my %sv_type_count;
-
   my @gens = qw/germline_recurrent germline_private somatic_tumour somatic_normal/;
   my @types = qw/DEL DUP INV BND TRA DUP:TANDEM CNV INS /;
 
@@ -666,13 +669,11 @@ sub summarise_variants {
   }
 
   for (keys %{ $SVs } ){
-
     my ( $chr, $start, $id, $ref, $alt, $quality_score, $filt, $info_block, $format_block, $tumour_info_block, $normal_info_block, $sv_type, $SV_length, $stop, $chr2, $SR, $PE, $ab, $filters, $genotype, $samples ) = @{ $SVs->{$_} };
 
     if ( $chromosome ){
       next if $chr ne $chromosome;
     }
-
     if ( $specified_region ){
       if ( ( $start < $query_start or $start > $query_stop ) and ( $stop < $query_stop or $stop > $query_stop ) ){
          next;
@@ -693,12 +694,9 @@ sub summarise_variants {
       next if $filter_switch;
     }
 
-
     $read_support = ( $SR + $PE );
     $support_by_chrom{$id} = [ $read_support, $sv_type, $chr, $SV_length, $start ];
-
     $sv_type_count{$genotype}{$sv_type}++;
-
   }
   print "\n";
 
@@ -1162,23 +1160,12 @@ sub read_depth_filter {
 }
 
 
-sub somatic_filter {
-  my ($id, $tumour_name, $control_name, $PON, $filter_reasons, $PON_info) = @_;
-
-  my %PON_info = % { $PON_info };
+sub genotype_filter {
+  my ($id, $genotype, $filter_reasons, $selected_genotype ) = @_;
   my @filter_reasons = @{ $filter_reasons };
-
-  for my $normal (keys %PON_info) {
-
-    if ( $PON_info{$normal}[1] eq '1/1' or $PON_info{$normal}[1] eq '0/1' ){
-      push @filter_reasons, "PON member '$normal' not homozygous for reference genotype=" . $PON_info{$normal}[1];
-    }
-    # Filter if any quality reads support var in any normal in PON
-    if ( $PON_info{$normal}[0] != 0){
-      push @filter_reasons, "PON member '$normal' has quality support for alternative genotype=" . $PON_info{$normal}[0];
+    if ( $genotype ne $selected_genotype ){
+      push @filter_reasons,  "Not $selected_genotype: genotype=" . $genotype;
     }
-
-  }
   return(\@filter_reasons);
 }
 
diff --git a/script/svParse.pl b/script/svParse.pl
index ec9730a..6c276f1 100755
--- a/script/svParse.pl
+++ b/script/svParse.pl
@@ -12,6 +12,7 @@
 
 use feature qw/ say /;
 use Data::Dumper;
+use Data::Printer;
 use File::Basename;
 use File::Path qw/ make_path / ;
 use File::Slurp;
@@ -25,7 +26,7 @@
 my $chromosome;
 my $method = "guess";
 my $print;
-my $exclude;
+my $exclude = "";
 my %filters;
 my $PON_print = 5;
 my %opt;
@@ -91,42 +92,28 @@
   }
 }
 
-my $filter_switch= 0;
-
-if ( scalar keys %filters > 0 ){
-  print "\n";
-  if ( exists $filters{'a'} ){
-    $filter_switch = 1;
-    my $filter_ref = allFilters($exclude, \@keys, \%filters);
-  }
-  elsif ( $filters{'su'} or $filters{'dp'} or $filters{'rdr'} or $filters{'sq'} or $filters{'chr'} or $filters{'g'} or $filters{'e'} or $filters{'n'} or $filters{'s'} ) {
-    say "Running in filter mode, using custom filters:";
-    say " o Read support >= $filters{'su'}" if $filters{'su'};
-    say " o Read depth (in both tumour and normal) > $filters{'dp'}" if $filters{'dp'};
-    say " o Read support / depth > $filters{'rdr'}" if $filters{'rdr'};
-    say " o SQ quality > $filters{'sq'}" if $filters{'sq'};
-    say " o Chromosomes: " . join(' ', @keys) if $filters{'chr'};
-    say " o Running in germline mode" if $filters{'g'};
-    say " o Running in somatic TUMOUR mode" if $filters{'s'};
-    say " o Running in somatic NORMAL mode" if $filters{'n'};
-    say " o Excluding calls overlapping: $exclude" if $filters{'e'};
-    $filter_switch = 1;
-  }
-  else {
-    my $illegals = join(",", keys %filters);
-    say "Illegal filter option used: '$illegals'. Please specify filters to run with (or use '-f or -f a' to run all defaults)";
-    say "Filter options available:";
-    say " o Read support: su=INT";
-    say " o Read depth: dp=INT";
-    say " o Read support / depth: rdr=FLOAT";
-    say " o SQ quality: sq=INT";
-    say " o Chromosomes: " . join(' ', @keys);
-    say " o Germline only: g=1";
-    say " o Exclude calls in bed file: e [bed file]";
-    die "Please check filter specification\n";
-     }
+my %legalOpts = ( 'su'  =>  1,
+                  'dp'  =>  1,
+                  'rdr' =>  1,
+                  'sq'  =>  1,
+                  'chr' =>  1,
+                  'gr'  =>  1,
+                  'gp'  =>  1,
+                  'st'  =>  1,
+                  'sn'  =>  1,
+                  'e'   =>  1,
+                  'a'   =>  1
+);
+
+my $filter_switch = 0;
+my $filter_ref;
+
+if ( exists $filters{'a'} ){
+  $filter_ref = allFilters(\%filters);
+  %filters = %{ $filter_ref };
 }
 
+($filter_switch, $filter_ref) = checkFilters(\%filters, \%legalOpts, 0, $exclude, \@keys) if scalar keys %filters > 0;
 my ($name, $extention) = split(/\.([^.]+)$/, basename($vcf_file), 2);
 
 print "\n";
@@ -148,21 +135,13 @@
 
   # Write out variants passing filters
   # Write out some useful info to txt file
-  if ( $filters{'g'} ){
-    print "Printing germline events\n";
-    svParser::print_variants( $SVs, $filtered_vars, $name, $filtered_out, 1 ) if $print;
-    svParser::write_summary( $SVs, $name, $summary_out, $method, 1) if $print;
-  }
-  else {
-    svParser::print_variants( $SVs, $filtered_vars, $name, $filtered_out, 0 ) if $print;
-    svParser::write_summary( $SVs, $name, $summary_out, $method, 0 ) if $print;
-  }
+  svParser::print_variants( $SVs, $filtered_vars, $name, $filtered_out, 0 ) if $print;
+  svParser::write_summary( $SVs, $name, $summary_out, $method, 0 ) if $print;
 }
 
 if ($method eq 'snp') {
   # Dump all variants to screen
   svParser::dump_variants( $SVs, $info, $filter_switch, $chromosome, $method) if $dump;
-
   if ($print or $id ){
     die "Print and get variants not supported for SNP data\n";
   }
@@ -200,21 +179,58 @@ sub testCalls {
 
 
 sub allFilters {
-  my ($exclude_file, $chroms, $f) = @_;
+  my $f = shift;
   my %filters = %{$f};
-  say "Running in filter mode, using all default filters:";
-  say " o Read support >= 4";
-  say " o Read depth (in both tumour and normal) > 10";
-  say " o Read support / depth > 0.1";
-  say " o SQ quality > 10";
-  say " o Chromosomes: " . join(' ', @{$chroms} );
-  say " o Excldung calls in regions: $exclude_file";
-
-  $filters{'su'} = 4;
+  $filters{'a'} = 1;
+  $filters{'su'}  = 4;
+  $filters{'dp'}  = 10;
+  $filters{'rdr'} = 0.1;
+  $filters{'sq'}  = 10;
+  $filters{'chr'} = 1;
   return(\%filters)
 }
 
 
+sub checkFilters {
+  my ($filter_given, $legalOpts, $filter_switch, $exclude, $chroms) = @_;
+  my %legalOpts = %{$legalOpts};
+  my %filters = %{$filter_given};
+  say "Running in filter mode, using custom filters:";
+
+  for my $k (keys %{ $filter_given } ){
+    if (exists $legalOpts{$k}){
+      explainFilters(\%legalOpts, $k, $exclude, $chroms);
+      $filter_switch = 1;
+    }
+    else {
+      printIllegals($k);
+    }
+  }
+  return($filter_switch, $filter_given);
+}
+
+sub explainFilters {
+  my ($legals, $filter_given, $exclude, $chroms) = @_;
+  my %legalOpts = %{ $legals };
+      say " o Read support >= $legalOpts{'su'}" if $filter_given eq 'su';
+      say " o Read depth (in both tumour and normal) > $legalOpts{'dp'}" if $filter_given eq 'dp';
+      say " o Read support / depth > $legalOpts{'rdr'}" if $filter_given eq 'rdr';
+      say " o SQ quality > $legalOpts{'sq'}" if $filter_given eq 'sq';
+      say " o Chromosomes: " . join(' ', @{$chroms}) if $filter_given eq 'chr';
+      say " o Running in germline PRIVATE mode" if $filter_given eq 'gp';
+      say " o Running in germline RECURRANT mode" if $filter_given eq 'gr';
+      say " o Running in somatic TUMOUR mode" if $filter_given eq 'st';
+      say " o Running in somatic NORMAL mode" if $filter_given eq 'sn';
+      say " o Excluding calls overlapping: $exclude" if $filter_given eq 'e';
+}
+
+sub printIllegals {
+  my $illegal_option = shift;
+  say "Illegal filter option used: '$illegal_option'. Please specify filters to run with (or use '-f or -f a' to run all defaults)";
+  die usage();
+}
+
+
 sub usage {
   print
 "
@@ -251,7 +267,10 @@ sub usage {
                             -f rdr=FLOAT [fraction of supporting reads/tumour depth - a value of 1 would mean all reads support variant]
                             -f sq=INT    [phred-scaled variant likelihood]
                             -f chr=1     [only show chromosomes in 'chroms.txt'. [Default use Drosophila chroms: 2L 2R 3L 3R 4 X Y]
-                            -f s=1       [only keep somatic tumour events]
+                            -f st=1      [only keep somatic tumour events]
+                            -f sn=1      [only keep somatic normal events]
+                            -f gp=1      [only keep germline private events]
+                            -f gr=1      [only keep germline recurrent events]
                             -f, -f a     [apply default filters: -f su=4 -f dp=10 -f rdr=0.1 -f sq=10 -f chr=1 ]
 "
 }