diff --git a/lib/npg_qc/autoqc/checks/genotype.pm b/lib/npg_qc/autoqc/checks/genotype.pm
index 3efb01e8..f2d19ff9 100644
--- a/lib/npg_qc/autoqc/checks/genotype.pm
+++ b/lib/npg_qc/autoqc/checks/genotype.pm
@@ -45,11 +45,11 @@ has '+file_type' => (default => $EXT,);
 has '+aligner'   => (default => 'fasta',);
 
 has 'irods' =>(
-   is       => 'ro',
-   isa      => 'WTSI::NPG::iRODS',
-   required => 1,
-   lazy     => 1,
-   builder  => '_build_irods',
+  is       => 'ro',
+  isa      => 'WTSI::NPG::iRODS',
+  required => 1,
+  lazy     => 1,
+  builder  => '_build_irods',
 );
 sub _build_irods {
   return WTSI::NPG::iRODS->new();
@@ -57,241 +57,241 @@ sub _build_irods {
 
 # you can override the executable name. May be useful for variants like "samtools_irods"
 has 'samtools_name' => (
-	is => 'ro',
-	isa => 'Str',
-	default => $SAMTOOLS_NAME,
+  is => 'ro',
+  isa => 'Str',
+  default => $SAMTOOLS_NAME,
 );
 
 has 'samtools' => (
-        is => 'ro',
-        isa => 'NpgCommonResolvedPathExecutable',
-        lazy_build => 1,
-        coerce => 1,
+  is => 'ro',
+  isa => 'NpgCommonResolvedPathExecutable',
+  lazy_build => 1,
+  coerce => 1,
 );
 sub _build_samtools {
-	my ($self) = @_;
-	return $self->samtools_name;
+  my ($self) = @_;
+  return $self->samtools_name;
 }
 
 # you can override the executable name. May be useful for variants like "samtools_irods"
 has 'bcftools_name' => (
-	is => 'ro',
-	isa => 'Str',
-	default => $BCFTOOLS_NAME,
+  is => 'ro',
+  isa => 'Str',
+  default => $BCFTOOLS_NAME,
 );
 
 has 'bcftools' => (
-        is => 'ro',
-        isa => 'NpgCommonResolvedPathExecutable',
-        lazy_build => 1,
-        coerce => 1,
+  is => 'ro',
+  isa => 'NpgCommonResolvedPathExecutable',
+  lazy_build => 1,
+  coerce => 1,
 );
 sub _build_bcftools {
-	my ($self) = @_;
-	return $self->bcftools_name;
+  my ($self) = @_;
+  return $self->bcftools_name;
 }
 
 # sequenom_plex - this specifies the source of the genotype data
 has 'sequenom_plex' => (
-	is => 'ro',
-	isa => 'Str',
+  is => 'ro',
+  isa => 'Str',
   writer => '_set_sequenom_plex',
-	default => $DEFAULT_QC_PLEX,
+  default => $DEFAULT_QC_PLEX,
 );
 
 # snp_call_set - this specifies the set of loci to be called. This may be
 #  the same for different sequenom_plex data sets. It is used to construct
 #  the name of some information files (positions, alleles, etc)
 has 'snp_call_set' => (
-	is => 'ro',
-	isa => 'Str',
+  is => 'ro',
+  isa => 'Str',
   writer => '_set_snp_call_set',
-	default => $DEFAULT_SNP_CALL_SET,
+  default => $DEFAULT_SNP_CALL_SET,
 );
 
 has 'aix_file' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_aix_file {
-	my $self = shift;
-	return $self->gt_db . q{.aix};
+  my $self = shift;
+  return $self->gt_db . q{.aix};
 }
 
 has 'gt_db' => (
-	is => 'ro',
-	isa => 'Str',
+  is => 'ro',
+  isa => 'Str',
   writer => '_set_gt_db',
-	lazy_build => 1,
+  lazy_build => 1,
 );
 sub _build_gt_db {
-	my $self = shift;
-	return catfile($self->genotypes_repository, $self->gt_db_base);
+  my $self = shift;
+  return catfile($self->genotypes_repository, $self->gt_db_base);
 }
 
 has 'gt_db_base' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_gt_db_base {
-	my $self = shift;
-	return sprintf q[%s_%s], $self->sequenom_plex, ${GENOTYPE_DATA};
+  my $self = shift;
+  return sprintf q[%s_%s], $self->sequenom_plex, ${GENOTYPE_DATA};
 }
 
 has 'reliable_read_depth' => (
-	is => 'ro',
-	isa => 'NpgTrackingNonNegativeInt',
-	default => $DEFAULT_RELIABLE_READ_DEPTH,
+  is => 'ro',
+  isa => 'NpgTrackingNonNegativeInt',
+  default => $DEFAULT_RELIABLE_READ_DEPTH,
 );
 
 has 'poss_dup_level' => (
-	is => 'ro',
-	isa => 'NpgTrackingNonNegativeInt',
-	default => $DEFAULT_POSS_DUP_LEVEL,
+  is => 'ro',
+  isa => 'NpgTrackingNonNegativeInt',
+  default => $DEFAULT_POSS_DUP_LEVEL,
 );
 
 has 'min_sample_call_rate' => (
-	is => 'ro',
-	isa => 'NpgTrackingNonNegativeInt',
-	default => $DEFAULT_MIN_SAMPLE_CALL_RATE,
+  is => 'ro',
+  isa => 'NpgTrackingNonNegativeInt',
+  default => $DEFAULT_MIN_SAMPLE_CALL_RATE,
 );
 
 has 'gt_pack_cmd' => (
-	is => 'ro',
-	isa => 'Str',
-	default => q{gt_pack},
+  is => 'ro',
+  isa => 'Str',
+  default => q{gt_pack},
 );
 
 has 'gt_pack_flags' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_gt_pack_flags {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	return q{ -o - -s 1 -f 1 -P } . $self->aix_file() . q{ };
+  return q{ -o - -s 1 -f 1 -P } . $self->aix_file() . q{ };
 }
 
 has 'gt_pack_args' => (
-	is => 'ro',
-	isa => 'Str',
-	default => ' - ',
+  is => 'ro',
+  isa => 'Str',
+  default => ' - ',
 );
 
 has 'find_gt_match_cmd' => (
-	is => 'ro',
-	isa => 'Str',
-	default => q{find_gt_match},
+  is => 'ro',
+  isa => 'Str',
+  default => q{find_gt_match},
 );
 
 has 'find_gt_match_flags' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_find_gt_match_flags {
-	my ($self) = @_;
-	return q{ -m } . $self->min_common_snps() . q{ -p -j -n "} . $self->sample_name . q{" -r } . $self->reliable_read_depth . q{ -d } . $self->poss_dup_level . q{ -s } . $self->min_sample_call_rate;
+  my ($self) = @_;
+  return q{ -m } . $self->min_common_snps() . q{ -p -j -n "} . $self->sample_name . q{" -r } . $self->reliable_read_depth . q{ -d } . $self->poss_dup_level . q{ -s } . $self->min_sample_call_rate;
 }
 
 has 'find_gt_match_args' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_find_gt_match_args {
-	my ($self) = @_;
-	return q{ - } . $self->gt_db();
+  my ($self) = @_;
+  return q{ - } . $self->gt_db();
 }
 
 has 'min_common_snps' => (
-	is => 'ro',
-	isa => 'NpgTrackingNonNegativeInt',
-	default => $DEFAULT_MIN_COMMON_SNPS,
+  is => 'ro',
+  isa => 'NpgTrackingNonNegativeInt',
+  default => $DEFAULT_MIN_COMMON_SNPS,
 );
 
 has 'sample_name'  => (
-	is => 'ro',
-	isa => 'Maybe[Str]',
+  is => 'ro',
+  isa => 'Maybe[Str]',
   writer => '_set_sample_name',
-	lazy_build => 1,
+  lazy_build => 1,
 );
 sub _build_sample_name {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	return $self->lims->sample_name;
+  return $self->lims->sample_name;
 }
 
 has 'reference_fasta' => (
-	is => 'ro',
-	isa => 'Maybe[Str]',
-	required => 0,
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Maybe[Str]',
+  required => 0,
+  lazy_build => 1,
 );
 sub _build_reference_fasta {
-	my ($self) = @_;
+  my ($self) = @_;
 
   my $href = { 'aligner' => $self->aligner, 'lims' => $self->lims, };
   my $ref  = $self->lims->gbs_plex_name ?
-      Moose::Meta::Class->create_anon_class(
-        roles => [qw/npg_tracking::data::gbs_plex::find/])->new_object($href)->refs->[0] :
-      $self->refs->[0];
+    Moose::Meta::Class->create_anon_class(
+      roles => [qw/npg_tracking::data::gbs_plex::find/])->new_object($href)->refs->[0] :
+    $self->refs->[0];
   return $ref;
 }
 
 has 'alignments_in_bam'  => (
-	is => 'ro',
-	isa => 'Maybe[Bool]',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Maybe[Bool]',
+  lazy_build => 1,
 );
 sub _build_alignments_in_bam {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	return $self->lims->alignments_in_bam;
+  return $self->lims->alignments_in_bam;
 }
 
 has 'bam_file' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_bam_file {
-	my ($self) = @_;
-	return $self->input_files->[0];
+  my ($self) = @_;
+  return $self->input_files->[0];
 }
 
 has 'bam_file_md5' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_bam_file_md5 {
-	my ($self) = @_;
-	my $bam_file = $self->bam_file;
-	my $md5 = q{};
+  my ($self) = @_;
+  my $bam_file = $self->bam_file;
+  my $md5 = q{};
 
-	if($bam_file) {
-		my $md5_file = "${bam_file}.md5";
+  if($bam_file) {
+    my $md5_file = "${bam_file}.md5";
 
-		if(-r $md5_file) {
-			open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
+    if(-r $md5_file) {
+      open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
 
-			$md5 = <$f>;
+      $md5 = <$f>;
 
-			close $f or croak "Failed to close $md5_file";
-		}
-	}
+      close $f or croak "Failed to close $md5_file";
+    }
+  }
 
-	return $md5;
+  return $md5;
 }
 
 has 'input_files_md5' => (
-	is => 'ro',
-	isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_input_files_md5 {
     my ($self) = @_;
@@ -300,35 +300,34 @@ sub _build_input_files_md5 {
 
     my @md5_vals = ();
     for my $input_file (@{$self->input_files}) {
-        $md5 = q{};
-        if ($input_file =~ /^irods:/smx) {
-            my $irods_filename = substr $input_file, $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH;  # strip leading "irods:"
-            try {
-                my $data_obj = WTSI::NPG::iRODS::DataObject->new(
-                    $self->irods, $irods_filename
-                );
-                $md5 = $data_obj->checksum;
-            } catch {
-                my $msg = 'Unable to find md5 checksum for '.
+      $md5 = q{};
+      if ($input_file =~ /^irods:/smx) {
+        my $irods_filename = substr $input_file, $IRODS_PREFIX_LEN_IS_THIS_READABLE_ENOUGH;  # strip leading "irods:"
+        try {
+          $md5 = WTSI::NPG::iRODS::DataObject->new(
+            $self->irods, $irods_filename
+          )->checksum;
+        } catch {
+          my $msg = 'Unable to find md5 checksum for '.
                     "iRODS file '$irods_filename': $_";
-                carp($msg);
-                $md5 = '0000000000000000';
-            }
-        } else {
-            my $md5_file = "${input_file}.md5";
-            if(-r $md5_file) {
-                open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
-                $md5 = <$f>;
-                chomp $md5;
-                close $f or croak "Failed to close $md5_file";
-            }
-            if (! $md5) {
-                my $msg = "Unable to read md5 checksum from file '$md5_file'";
-                carp($msg);
-                $md5 = '0000000000000000';
-            }
+          carp($msg);
+          $md5 = '0000000000000000';
+        }
+      } else {
+        my $md5_file = "${input_file}.md5";
+        if(-r $md5_file) {
+          open my $f, '<', $md5_file or croak "$md5_file readable, but open fails";
+          $md5 = <$f>;
+          chomp $md5;
+          close $f or croak "Failed to close $md5_file";
+        }
+        if (! $md5) {
+          my $msg = "Unable to read md5 checksum from file '$md5_file'";
+          carp($msg);
+          $md5 = '0000000000000000';
         }
-        push @md5_vals, $md5;
+      }
+      push @md5_vals, $md5;
     }
 
     return join q[;], @md5_vals;
@@ -338,27 +337,27 @@ sub _build_input_files_md5 {
 # pos_snpname_map_fn should be either specified at instantiation or implied by the Sequenom plex and reference genome
 #####################################################################################################################
 has 'pos_snpname_map_fn' => (
-        is => 'ro',
-        isa => 'NpgTrackingReadableFile',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'NpgTrackingReadableFile',
+  lazy_build => 1,
 );
 sub _build_pos_snpname_map_fn {
-	my ($self) = @_;
-	my $genotypes_repository = $self->genotypes_repository;
-	my $reference = $self->reference_fasta;
-	my $ref_to_snppos_suffix_map = $self->_ref_to_snppos_suffix_map;
+  my ($self) = @_;
+  my $genotypes_repository = $self->genotypes_repository;
+  my $reference = $self->reference_fasta;
+  my $ref_to_snppos_suffix_map = $self->_ref_to_snppos_suffix_map;
 
-	my $chrconv_suffix = $ref_to_snppos_suffix_map->{basename($reference)};
+  my $chrconv_suffix = $ref_to_snppos_suffix_map->{basename($reference)};
 
 
-	if(!defined $reference || !defined $chrconv_suffix) {
-		return;
-	}
+  if(!defined $reference || !defined $chrconv_suffix) {
+    return;
+  }
 
-	my $fn = sprintf '%s_chrpos_snpname_map_%s.tsv', $self->snp_call_set, $chrconv_suffix;
-	my $pos_snpname_map_fn = catfile($genotypes_repository, $fn);
+  my $fn = sprintf '%s_chrpos_snpname_map_%s.tsv', $self->snp_call_set, $chrconv_suffix;
+  my $pos_snpname_map_fn = catfile($genotypes_repository, $fn);
 
-	return $pos_snpname_map_fn;
+  return $pos_snpname_map_fn;
 }
 
 ##################################################################################################################
@@ -367,86 +366,86 @@ sub _build_pos_snpname_map_fn {
 #  implied by the Sequenom plex and reference genome.
 ##################################################################################################################
 has 'chrname_conv_fn' => (
-        is => 'ro',
-        isa => 'Str',
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'Str',
+  lazy_build => 1,
 );
 sub _build_chrname_conv_fn {
-	my ($self) = @_;
-	my $genotypes_repository = $self->genotypes_repository;
+  my ($self) = @_;
+  my $genotypes_repository = $self->genotypes_repository;
 
-	my $fn = $genotypes_repository . q[/chrconv_map_v2.json];
+  my $fn = $genotypes_repository . q[/chrconv_map_v2.json];
 
-	return $fn;
+  return $fn;
 }
 
 ##############################################################################################
 # report_aux_data tells bam_genotype to include read depth and genotype likelihood information
 ##############################################################################################
 has 'report_aux_data' => (
-	is => 'ro',
-	isa => 'Bool',
-	default => 1,
+  is => 'ro',
+  isa => 'Bool',
+  default => 1,
 );
 
 has 'bam_genotype' => (
-	is => 'ro',
-	isa => 'npg_qc::utils::bam_genotype',
-	handles => { tsv_genotype => 'genotype', json_genotype => 'json_genotype', },
-	lazy_build => 1,
+  is => 'ro',
+  isa => 'npg_qc::utils::bam_genotype',
+  handles => { tsv_genotype => 'genotype', json_genotype => 'json_genotype', },
+  lazy_build => 1,
 );
 sub _build_bam_genotype {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	my %bg_params = (sample_name => $self->sample_name, plex => $self->sequenom_plex, reference => $self->reference_fasta, pos_snpname_map_filename => $self->pos_snpname_map_fn, report_aux_data => $self->report_aux_data, samtools_name => $self->samtools_name, bcftools => $self->bcftools, bcftools_name => $self->bcftools_name, );
+  my %bg_params = (sample_name => $self->sample_name, plex => $self->sequenom_plex, reference => $self->reference_fasta, pos_snpname_map_filename => $self->pos_snpname_map_fn, report_aux_data => $self->report_aux_data, samtools_name => $self->samtools_name, bcftools => $self->bcftools, bcftools_name => $self->bcftools_name, );
 
-	$bg_params{bam_file_list} = $self->input_files;
+  $bg_params{bam_file_list} = $self->input_files;
 
-	return npg_qc::utils::bam_genotype->new(%bg_params);
+  return npg_qc::utils::bam_genotype->new(%bg_params);
 }
 
 override 'can_run' => sub {
-	my $self = shift;
-
-	if(!defined $self->sample_name) {
-		$self->result->add_comment('No sample name specified');
-		return 0;
-	}
-
-	if(!$self->alignments_in_bam) {
-		$self->result->add_comment('alignments_in_bam is false');
-		return 0;
-	}
-
-	if(!defined($self->reference_fasta) || (! -r $self->reference_fasta)) {
-		$self->result->add_comment('Reference genome missing or unreadable');
-		return 0;
-	}
-
- 	# make sure that the bam file is aligned with one of the recognised human references
-	if(! any { $_ eq fileparse($self->reference_fasta); } (keys %{$self->_ref_to_snppos_suffix_map})) {
-		$self->result->add_comment('Specified reference genome may be non-human');
-		return 0;
- 	}
-
- 	return 1;
+  my $self = shift;
+
+  if(!defined $self->sample_name) {
+    $self->result->add_comment('No sample name specified');
+    return 0;
+  }
+
+  if(!$self->alignments_in_bam) {
+    $self->result->add_comment('alignments_in_bam is false');
+    return 0;
+  }
+
+  if(!defined($self->reference_fasta) || (! -r $self->reference_fasta)) {
+    $self->result->add_comment('Reference genome missing or unreadable');
+    return 0;
+  }
+
+   # make sure that the bam file is aligned with one of the recognised human references
+  if(! any { $_ eq fileparse($self->reference_fasta); } (keys %{$self->_ref_to_snppos_suffix_map})) {
+    $self->result->add_comment('Specified reference genome may be non-human');
+    return 0;
+   }
+
+   return 1;
 };
 
 override 'execute' => sub {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	try {
-		super();
-	} catch {
-		my $e = $_;
-		if(none {/\Airods:/smx} @{$self->input_files}) { # we might be given files from iRODS
-			croak $_;
-		}
-	};
+  try {
+    super();
+  } catch {
+    my $e = $_;
+    if(none {/\Airods:/smx} @{$self->input_files}) { # we might be given files from iRODS
+      croak $_;
+    }
+  };
 
-	if(!$self->can_run()) {
-		return 1;
-	}
+  if(!$self->can_run()) {
+    return 1;
+  }
 
   # over-ride if geno_refset available
   if($self->geno_refset && !$self->lims->gbs_plex_name) {
@@ -454,114 +453,114 @@ override 'execute' => sub {
   }
 
   # run check
-	my $gt_check_cmd = sprintf
-			q{set -o pipefail && printf "%s" | %s %s %s | %s %s %s},
-			$self->tsv_genotype,
-			$self->gt_pack_cmd(),
-			$self->gt_pack_flags(),
-			$self->gt_pack_args,
-			$self->find_gt_match_cmd(),
-			$self->find_gt_match_flags(),
-			$self->find_gt_match_args()
-		;
-
-	open my $f, q{-|}, qw{bash -c}, qq{$gt_check_cmd} or croak 'Failed to execute check';
-
-	my $json_results = <$f>;
-
-	close $f or croak 'Failed to close check';
-
-	if(!$json_results) {
-		croak 'No results from check';
-	}
-
-	my $result = from_json($json_results);
-
-	my $gt_caller_info = $self->current_version($self->samtools);
-	$self->result->set_info('Caller', $self->samtools);
-	$self->result->set_info('Caller_version', $gt_caller_info);
-
-	$self->result->genotype_data_set($result->{genotype_data_set});
-
-	$self->result->snp_call_set($self->snp_call_set);
-
-	my $bam_file_leaves = join q[;], (map { basename($_); } @{$self->input_files});
-	$self->result->bam_file($bam_file_leaves);    # name of result attribute should probably be changed to reflect the possibility of more than one bam file; check qc db
-
-	$self->result->bam_file_md5($self->input_files_md5);
-
-	my $reference_leaf = fileparse($self->reference_fasta);
-	$self->result->reference($reference_leaf);
-
-	$self->result->bam_call_count($self->json_genotype->{number_of_calls});
-
-	my $bam_call_string = join q{}, map { $_->{call}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
-	$self->result->bam_call_string($bam_call_string);
-
-	my $bam_gt_depths_string = join q{;}, map { defined $_->{depth}? $_->{depth}: q{0}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
-	$self->result->bam_gt_depths_string($bam_gt_depths_string);
-
-	my $bam_gt_likelihood_string = join q{;}, map { defined $_->{gt_pl}? $_->{gt_pl}: q{0}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
-	$self->result->bam_gt_likelihood_string($bam_gt_likelihood_string);
-
-	$self->result->expected_sample_name($self->sample_name);
-	$self->result->search_parameters($result->{params});
-	$self->result->sample_name_match((grep { $_->{match_type} eq 'SampleNameMatch'; } @{$result->{comp_results}})[0]);
-	$self->result->sample_name_relaxed_match((grep { $_->{match_type} eq 'RM_SampleNameMatch'; } @{$result->{comp_results}})[0]);
-
-	my @high_concordant_pos_dups = grep { $_->{match_type} eq 'HIGHconcordantPosDupDnaDiff' and $_->{matched_sample_name} ne $self->sample_name; } @{$result->{comp_results}};
-	@high_concordant_pos_dups = reverse sort { $a->{match_pct} <=> $b->{match_pct}; } @high_concordant_pos_dups;
-	my $top_idx;
-	$top_idx = _cap_range(\@high_concordant_pos_dups, $MAX_ALT_MATCHES);
-	if ($top_idx > 0) {
-		@high_concordant_pos_dups = @high_concordant_pos_dups[0..$top_idx];
-	}
-	if(@high_concordant_pos_dups) {
-		$self->result->alternate_matches([@high_concordant_pos_dups]);
-	}
-
-	$self->result->alternate_match_count(0);
-	if(defined $self->result->alternate_matches) {
-		$self->result->alternate_match_count(scalar @{$self->result->alternate_matches});
-	}
-
-	my @rm_high_concordant_pos_dups = grep { $_->{match_type} eq 'RM_HIGHconcordantPosDupDnaDiff' and $_->{matched_sample_name} ne $self->sample_name; } @{$result->{comp_results}};
-	@rm_high_concordant_pos_dups = reverse sort { $a->{match_pct} <=> $b->{match_pct}; } @rm_high_concordant_pos_dups;
-	$top_idx = _cap_range(\@rm_high_concordant_pos_dups, $MAX_ALT_MATCHES);
-	if($top_idx > 0) {
-		@rm_high_concordant_pos_dups = @rm_high_concordant_pos_dups[0..$top_idx];
-	}
-	if(@rm_high_concordant_pos_dups) {
-		$self->result->alternate_relaxed_matches([@rm_high_concordant_pos_dups]);
-	}
-
-	$self->result->alternate_relaxed_match_count(0);
-	if(defined $self->result->alternate_relaxed_matches) {
-		$self->result->alternate_relaxed_match_count(scalar @{$self->result->alternate_relaxed_matches()});
-	}
-
-	if(defined $self->result->sample_name_relaxed_match and $self->result->sample_name_relaxed_match->{common_snp_count} >= $DEFAULT_MIN_COMMON_SNPS) {
-		if($self->result->sample_name_relaxed_match->{match_pct} > $MATCH_PASS_THRESHOLD) {
-			$self->result->pass(1);
-		}
-		elsif($self->result->sample_name_relaxed_match->{match_pct} < $MATCH_FAIL_THRESHOLD) {
-			$self->result->pass(0);
-		}
-	}
-
-	return 1;
+  my $gt_check_cmd = sprintf
+      q{set -o pipefail && printf "%s" | %s %s %s | %s %s %s},
+      $self->tsv_genotype,
+      $self->gt_pack_cmd(),
+      $self->gt_pack_flags(),
+      $self->gt_pack_args,
+      $self->find_gt_match_cmd(),
+      $self->find_gt_match_flags(),
+      $self->find_gt_match_args()
+    ;
+
+  open my $f, q{-|}, qw{bash -c}, qq{$gt_check_cmd} or croak 'Failed to execute check';
+
+  my $json_results = <$f>;
+
+  close $f or croak 'Failed to close check';
+
+  if(!$json_results) {
+    croak 'No results from check';
+  }
+
+  my $result = from_json($json_results);
+
+  my $gt_caller_info = $self->current_version($self->samtools);
+  $self->result->set_info('Caller', $self->samtools);
+  $self->result->set_info('Caller_version', $gt_caller_info);
+
+  $self->result->genotype_data_set($result->{genotype_data_set});
+
+  $self->result->snp_call_set($self->snp_call_set);
+
+  my $bam_file_leaves = join q[;], (map { basename($_); } @{$self->input_files});
+  $self->result->bam_file($bam_file_leaves);    # name of result attribute should probably be changed to reflect the possibility of more than one bam file; check qc db
+
+  $self->result->bam_file_md5($self->input_files_md5);
+
+  my $reference_leaf = fileparse($self->reference_fasta);
+  $self->result->reference($reference_leaf);
+
+  $self->result->bam_call_count($self->json_genotype->{number_of_calls});
+
+  my $bam_call_string = join q{}, map { $_->{call}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
+  $self->result->bam_call_string($bam_call_string);
+
+  my $bam_gt_depths_string = join q{;}, map { defined $_->{depth}? $_->{depth}: q{0}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
+  $self->result->bam_gt_depths_string($bam_gt_depths_string);
+
+  my $bam_gt_likelihood_string = join q{;}, map { defined $_->{gt_pl}? $_->{gt_pl}: q{0}; } @{$self->json_genotype->{calls}}{sort keys %{$self->json_genotype->{calls}}};
+  $self->result->bam_gt_likelihood_string($bam_gt_likelihood_string);
+
+  $self->result->expected_sample_name($self->sample_name);
+  $self->result->search_parameters($result->{params});
+  $self->result->sample_name_match((grep { $_->{match_type} eq 'SampleNameMatch'; } @{$result->{comp_results}})[0]);
+  $self->result->sample_name_relaxed_match((grep { $_->{match_type} eq 'RM_SampleNameMatch'; } @{$result->{comp_results}})[0]);
+
+  my @high_concordant_pos_dups = grep { $_->{match_type} eq 'HIGHconcordantPosDupDnaDiff' and $_->{matched_sample_name} ne $self->sample_name; } @{$result->{comp_results}};
+  @high_concordant_pos_dups = reverse sort { $a->{match_pct} <=> $b->{match_pct}; } @high_concordant_pos_dups;
+  my $top_idx;
+  $top_idx = _cap_range(\@high_concordant_pos_dups, $MAX_ALT_MATCHES);
+  if ($top_idx > 0) {
+    @high_concordant_pos_dups = @high_concordant_pos_dups[0..$top_idx];
+  }
+  if(@high_concordant_pos_dups) {
+    $self->result->alternate_matches([@high_concordant_pos_dups]);
+  }
+
+  $self->result->alternate_match_count(0);
+  if(defined $self->result->alternate_matches) {
+    $self->result->alternate_match_count(scalar @{$self->result->alternate_matches});
+  }
+
+  my @rm_high_concordant_pos_dups = grep { $_->{match_type} eq 'RM_HIGHconcordantPosDupDnaDiff' and $_->{matched_sample_name} ne $self->sample_name; } @{$result->{comp_results}};
+  @rm_high_concordant_pos_dups = reverse sort { $a->{match_pct} <=> $b->{match_pct}; } @rm_high_concordant_pos_dups;
+  $top_idx = _cap_range(\@rm_high_concordant_pos_dups, $MAX_ALT_MATCHES);
+  if($top_idx > 0) {
+    @rm_high_concordant_pos_dups = @rm_high_concordant_pos_dups[0..$top_idx];
+  }
+  if(@rm_high_concordant_pos_dups) {
+    $self->result->alternate_relaxed_matches([@rm_high_concordant_pos_dups]);
+  }
+
+  $self->result->alternate_relaxed_match_count(0);
+  if(defined $self->result->alternate_relaxed_matches) {
+    $self->result->alternate_relaxed_match_count(scalar @{$self->result->alternate_relaxed_matches()});
+  }
+
+  if(defined $self->result->sample_name_relaxed_match and $self->result->sample_name_relaxed_match->{common_snp_count} >= $DEFAULT_MIN_COMMON_SNPS) {
+    if($self->result->sample_name_relaxed_match->{match_pct} > $MATCH_PASS_THRESHOLD) {
+      $self->result->pass(1);
+    }
+    elsif($self->result->sample_name_relaxed_match->{match_pct} < $MATCH_FAIL_THRESHOLD) {
+      $self->result->pass(0);
+    }
+  }
+
+  return 1;
 };
 
 sub _cap_range {
-	my ($arr_ref, $max_value) = @_;
-	my $top_value;
+  my ($arr_ref, $max_value) = @_;
+  my $top_value;
 
-	$top_value = $#{$arr_ref};
-	if($top_value >= $max_value) {
-		$top_value = $max_value - 1;
-	}
+  $top_value = $#{$arr_ref};
+  if($top_value >= $max_value) {
+    $top_value = $max_value - 1;
+  }
 
-	return $top_value;
+  return $top_value;
 }
 
 ####################
@@ -574,28 +573,28 @@ sub _cap_range {
 #  or 'GRCh38' (meaning chr1, chr2, ...)
 ###############################################################################################################
 has '_ref_to_snppos_suffix_map' => (
-	isa => 'HashRef',
-	is => 'ro',
-	lazy_build => 1,
+  isa => 'HashRef',
+  is => 'ro',
+  lazy_build => 1,
 );
 sub _build__ref_to_snppos_suffix_map {
-	my ($self) = @_;
+  my ($self) = @_;
 
-	my $chrconv_fn = $self->chrname_conv_fn;
+  my $chrconv_fn = $self->chrname_conv_fn;
 
-	if($chrconv_fn and -f $chrconv_fn) { # if a map file is available, use it
-		my $chrconv_map = {};
-                my $s = read_file($chrconv_fn);
-                if($s) {
-                        my $json = from_json($s);
-			$chrconv_map = $json->{ref_chrconv_map};
-                }
+  if($chrconv_fn and -f $chrconv_fn) { # if a map file is available, use it
+    my $chrconv_map = {};
+    my $s = read_file($chrconv_fn);
+    if($s) {
+      my $json = from_json($s);
+      $chrconv_map = $json->{ref_chrconv_map};
+    }
     return $chrconv_map;
-        }
-	else { # default to these values when map file is unavailable
-		Readonly::Scalar my $NO_CHR_SUFFIX => '1000Genomes';
-		Readonly::Scalar my $USE_CHR_SUFFIX => 'GRCh37';
-		Readonly::Scalar my $USE_GRCH38_CHR_SUFFIX => 'GRCh38';
+
+  } else { # default to these values when map file is unavailable
+    Readonly::Scalar my $NO_CHR_SUFFIX => '1000Genomes';
+    Readonly::Scalar my $USE_CHR_SUFFIX => 'GRCh37';
+    Readonly::Scalar my $USE_GRCH38_CHR_SUFFIX => 'GRCh38';
 
     my $ref_to_snppos_suffix_map = {
       q{human_g1k_v37.fasta} => $NO_CHR_SUFFIX,
@@ -609,8 +608,8 @@ sub _build__ref_to_snppos_suffix_map {
       q{Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa} => $USE_GRCH38_CHR_SUFFIX,
     };
 
-		return $ref_to_snppos_suffix_map;
-	}
+    return $ref_to_snppos_suffix_map;
+  }
 }
 
 ###################################################################
@@ -618,22 +617,22 @@ sub _build__ref_to_snppos_suffix_map {
 ###################################################################
 
 has 'geno_refset' => (
-	is       => 'ro',
-	isa      => 'Str | Undef',
-	lazy     => 1,
+  is       => 'ro',
+  isa      => 'Str | Undef',
+  lazy     => 1,
   builder  => q[_build_geno_refset],
 );
 sub _build_geno_refset {
-	my ($self) = @_;
+  my ($self) = @_;
   my $ref = $self->_get_grfind;
   return $ref->geno_refset_genotype_base ?
       $ref->geno_refset_genotype_base : q[];
 }
 
 has 'alternate_sample_name' => (
-	is       => 'ro',
-	isa      => 'Str | Undef',
-	lazy     => 1,
+  is       => 'ro',
+  isa      => 'Str | Undef',
+  lazy     => 1,
   builder  => q[_build_alternate_sample_name],
 );
 sub _build_alternate_sample_name {
@@ -758,7 +757,7 @@ Kevin Lewis, kl2
 
 Copyright (C) 2018 GRL
 
-    This file is part of NPG.
+This file is part of NPG.
 
 NPG is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
diff --git a/t/60-autoqc-results-result.t b/t/60-autoqc-results-result.t
index 2537334c..6fa1ff8f 100644
--- a/t/60-autoqc-results-result.t
+++ b/t/60-autoqc-results-result.t
@@ -96,7 +96,7 @@ subtest 'saving object to and loading from file' => sub {
     $r->store($saved_path);
     my $json = $r->freeze();
     is ($r->_id_run_common, 2549, 'one of private attributes is set');
-    unlike($json, qr/\"_[:a-z:]/, 'private attributes are not serialized'); 
+    unlike($json, qr/\"_[a-z]/, 'private attributes are not serialized'); 
     delete $r->{'filename_root'};
     my $saved_r = npg_qc::autoqc::results::result->load($saved_path);
     sleep 1;