diff --git a/definitions/install_parameters.yaml b/definitions/install_parameters.yaml
index 3d3b10faa..2f03a45fd 100644
--- a/definitions/install_parameters.yaml
+++ b/definitions/install_parameters.yaml
@@ -73,6 +73,7 @@ rd_dna:
     - cnvnator
     - cyrius
     - deepvariant
+    - deeptrio
     - delly
     - expansionhunter
     - fastqc
diff --git a/definitions/rd_dna_initiation_map.yaml b/definitions/rd_dna_initiation_map.yaml
index fed2259df..cd9837604 100644
--- a/definitions/rd_dna_initiation_map.yaml
+++ b/definitions/rd_dna_initiation_map.yaml
@@ -55,6 +55,7 @@ CHAIN_ALL:
     - PARALLEL:
       - CHAIN_DEEPVAR:
         - deepvariant
+        - deeptrio
         - glnexus_merge
       - GATK_HAPLOTYPECALLER:
         - gatk_haplotypecaller
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index 44e57632a..9819745a0 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -83,6 +83,7 @@ gpu_capable_executables:
   data_type: ARRAY
   default:
     - run_deepvariant
+    - run_deeptrio
     - call_variants
   type: mip
 ## HumanGenomeReference
@@ -150,6 +151,7 @@ recipe_core_number:
     chromograph_rhoviz: 1
     chromograph_upd: 1
     cnvnator_ar: 13
+    deeptrio: 36
     deepvariant: 36
     delly_call: 36
     delly_reformat: 13
@@ -214,6 +216,7 @@ recipe_gpu_number:
   data_type: HASH
   default:
     deepvariant: 1
+    deeptrio: 1
   type: mip
 set_recipe_gpu_number:
   associated_recipe:
@@ -279,6 +282,7 @@ recipe_time:
     chromograph_rhoviz: 1
     chromograph_upd: 1
     cnvnator_ar: 1
+    deeptrio: 15
     deepvariant: 10
     delly_call: 20
     delly_reformat: 7
@@ -511,6 +515,17 @@ deepvariant:
   program_executables:
     - run_deepvariant
   type: recipe
+deeptrio:
+  analysis_mode: case
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  file_tag: _deeptrio
+  outfile_suffix: ".g.vcf.gz"
+  program_executables:
+    - run_deeptrio
+  type: recipe
 glnexus_merge:
   analysis_mode: case
   associated_recipe:
diff --git a/lib/MIP/Cli/Mip/Install.pm b/lib/MIP/Cli/Mip/Install.pm
index 4b2ba009c..1d73b5083 100644
--- a/lib/MIP/Cli/Mip/Install.pm
+++ b/lib/MIP/Cli/Mip/Install.pm
@@ -131,8 +131,8 @@ sub _build_usage {
                 enum(
                     [
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
-                          chromograph cnvnator cyrius deepvariant delly expansionhunter fastqc gatk gatk4
-                          genmod gffcompare glnexus htslib manta mip mip_scripts multiqc peddy picard plink
+                          chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk 
+                          gatk4 genmod gffcompare glnexus htslib manta mip mip_scripts multiqc peddy picard plink
                           preseq python rhocall rseqc rtg-tools salmon sambamba smncopynumbercaller star
                           star-fusion stranger stringtie svdb telomerecat tiddit trim-galore ucsc upd
                           utilities varg vcf2cytosure vcfanno vep vts }
@@ -153,8 +153,8 @@ sub _build_usage {
                 enum(
                     [
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
-                          chromograph cnvnator cyrius deepvariant delly expansionhunter fastqc gatk gatk4
-                          genmod gffcompare glnexus htslib manta mip mip_scripts multiqc peddy picard plink
+                          chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk 
+                          gatk4 genmod gffcompare glnexus htslib manta mip mip_scripts multiqc peddy picard plink
                           preseq python rhocall rseqc rtg-tools salmon sambamba smncopynumbercaller star
                           star-fusion stranger stringtie svdb telomerecat tiddit trim-galore ucsc upd
                           utilities varg vcf2cytosure vcfanno vep vts }
diff --git a/lib/MIP/Pedigree.pm b/lib/MIP/Pedigree.pm
index 188c735ee..47f48a091 100644
--- a/lib/MIP/Pedigree.pm
+++ b/lib/MIP/Pedigree.pm
@@ -34,6 +34,7 @@ BEGIN {
       create_fam_file
       get_is_trio
       gatk_pedigree_flag
+      has_duo
       has_trio
       is_sample_proband_in_trio
       parse_pedigree
@@ -47,6 +48,7 @@ BEGIN {
 }
 
 ## Constants
+Readonly my $DUO_MEMBERS_COUNT  => 2;
 Readonly my $TRIO_MEMBERS_COUNT => 3;
 
 sub check_founder_id {
@@ -490,6 +492,62 @@ sub get_is_trio {
     return;
 }
 
+sub has_duo {
+
+## Function  : Check if case has a parent-child duo and child is affected
+## Returns   : 0 | 1
+## Arguments : $active_parameter_href => Active parameters for this analysis hash {REF}
+##           : $sample_info_href      => Info on samples and case hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $active_parameter_href;
+    my $sample_info_href;
+
+    my $tmpl = {
+        active_parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$active_parameter_href,
+            strict_type => 1,
+        },
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Sample_info qw{ get_pedigree_sample_id_attributes };
+
+    ## Has two samples
+    return 0
+      if ( scalar @{ $active_parameter_href->{sample_ids} } != $DUO_MEMBERS_COUNT );
+
+  SAMPLE_ID:
+    foreach my $sample_id ( @{ $active_parameter_href->{sample_ids} } ) {
+
+        my %sample_attributes = get_pedigree_sample_id_attributes(
+            {
+                sample_id        => $sample_id,
+                sample_info_href => $sample_info_href,
+            }
+        );
+
+        ## Find a child
+        next SAMPLE_ID if ( not( $sample_attributes{father} or $sample_attributes{mother} ) );
+
+        return 1 if ( $sample_attributes{phenotype} eq q{affected} );
+    }
+    return 0;
+}
+
 sub has_trio {
 
 ## Function  : Check if case has trio
diff --git a/lib/MIP/Program/Deeptrio.pm b/lib/MIP/Program/Deeptrio.pm
new file mode 100644
index 000000000..abb0798da
--- /dev/null
+++ b/lib/MIP/Program/Deeptrio.pm
@@ -0,0 +1,249 @@
+package MIP::Program::Deeptrio;
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use utf8;
+use warnings;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+
+## MIPs lib/
+use MIP::Constants qw{ $EQUALS $SPACE };
+use MIP::Environment::Executable qw{ get_executable_base_command };
+use MIP::Unix::Standard_streams qw{ unix_standard_streams };
+use MIP::Unix::Write_to_file qw{ unix_write_to_file };
+
+BEGIN {
+    require Exporter;
+    use base qw{ Exporter };
+
+    # Functions and variables which can be optionally exported
+    our @EXPORT_OK = qw{ deeptrio };
+}
+
+sub deeptrio {
+
+## Function : Perl wrapper for generic commands module
+## Returns  : @commands
+## Arguments: $bedfile                => Bed file containing the list of regions we want to process
+##          : $filehandle             => Filehandle to write to
+##          : $model_type             => Type of model to use for variant calling. Allowed values WES, WGS, or PACBIO
+##          : $num_shards             => Number of files the input is split into for the make examples step
+##          : $output_gvcf_child      => Path to output gvcf file for the child in a duo or trio
+##          : $output_gvcf_parent1    => Path to output gvcf for a parent in a duo or a trio
+##          : $output_gvcf_parent2    => Path to output gvcf for a parent in trio
+##          : $output_vcf_child       => Path to output vcf file for the child in a duo or trio
+##          : $output_vcf_parent1     => Path to output vcf for a parent in a duo or trio
+##          : $output_vcf_parent2     => Path to output vcf for a parent in trio
+##          : $reads_child            => Path to input bam for the child in a duo or trio
+##          : $reads_parent1          => Path to input bam for a parent in a duo or trio
+##          : $reads_parent2          => Path to input bam for a parent in trio
+##          : $referencefile_path     => Path to genome reference
+##          : $sample_name_child      => Sample name for the child in a duo or trio
+##          : $sample_name_parent1    => Sample name for a parent in a duo or trio
+##          : $sample_name_parent2    => Sample name for a parent in trio
+##          : $stderrfile_path        => Stderrfile path
+##          : $stderrfile_path_append => Append stderr info to file path
+##          : $stdinfile_path         => Stdinfile path
+##          : $stdoutfile_path        => Stdoutfile path
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $bedfile;
+    my $filehandle;
+    my $model_type;
+    my $num_shards;
+    my $output_gvcf_child;
+    my $output_gvcf_parent1;
+    my $output_gvcf_parent2;
+    my $output_vcf_child;
+    my $output_vcf_parent1;
+    my $output_vcf_parent2;
+    my $reads_child;
+    my $reads_parent1;
+    my $reads_parent2;
+    my $referencefile_path;
+    my $sample_name_child;
+    my $sample_name_parent1;
+    my $sample_name_parent2;
+    my $stderrfile_path;
+    my $stderrfile_path_append;
+    my $stdinfile_path;
+    my $stdoutfile_path;
+
+    my $tmpl = {
+        bedfile => {
+            defined     => 1,
+            store       => \$bedfile,
+            strict_type => 1,
+        },
+        filehandle => {
+            store => \$filehandle,
+        },
+        model_type => {
+            allow       => [qw{ WES WGS PACBIO }],
+            defined     => 1,
+            required    => 1,
+            store       => \$model_type,
+            strict_type => 1,
+        },
+        num_shards => {
+            allow       => qr/ \A \d+ \z /xms,
+            required    => 1,
+            store       => \$num_shards,
+            strict_type => 1,
+        },
+        output_gvcf_child => {
+            defined     => 1,
+            required    => 1,
+            store       => \$output_gvcf_child,
+            strict_type => 1,
+        },
+        output_gvcf_parent1 => {
+            defined     => 1,
+            required    => 1,
+            store       => \$output_gvcf_parent1,
+            strict_type => 1,
+        },
+        output_gvcf_parent2 => {
+            store       => \$output_gvcf_parent2,
+            strict_type => 1,
+        },
+        output_vcf_child => {
+            defined     => 1,
+            required    => 1,
+            store       => \$output_vcf_child,
+            strict_type => 1,
+        },
+        output_vcf_parent1 => {
+            defined     => 1,
+            required    => 1,
+            store       => \$output_vcf_parent1,
+            strict_type => 1,
+        },
+        output_vcf_parent2 => {
+            store       => \$output_vcf_parent2,
+            strict_type => 1,
+        },
+        reads_child => {
+            defined     => 1,
+            required    => 1,
+            store       => \$reads_child,
+            strict_type => 1,
+        },
+        reads_parent1 => {
+            defined     => 1,
+            required    => 1,
+            store       => \$reads_parent1,
+            strict_type => 1,
+        },
+        reads_parent2 => {
+            store       => \$reads_parent2,
+            strict_type => 1,
+        },
+        referencefile_path => {
+            defined     => 1,
+            required    => 1,
+            store       => \$referencefile_path,
+            strict_type => 1,
+        },
+        sample_name_child => {
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_name_child,
+            strict_type => 1,
+        },
+        sample_name_parent1 => {
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_name_parent1,
+            strict_type => 1,
+        },
+        sample_name_parent2 => {
+            store       => \$sample_name_parent2,
+            strict_type => 1,
+        },
+        stderrfile_path => {
+            store       => \$stderrfile_path,
+            strict_type => 1,
+        },
+        stderrfile_path_append => {
+            store       => \$stderrfile_path_append,
+            strict_type => 1,
+        },
+        stdinfile_path => {
+            store       => \$stdinfile_path,
+            strict_type => 1,
+        },
+        stdoutfile_path => {
+            store       => \$stdoutfile_path,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my @commands =
+      ( get_executable_base_command( { base_command => q{run_deeptrio}, } ), );
+
+    push @commands, q{--model_type} . $SPACE . $model_type;
+    push @commands, q{--ref} . $SPACE . $referencefile_path;
+    push @commands, q{--num_shards} . $SPACE . $num_shards;
+
+    ## Child
+    push @commands, q{--sample_name_child} . $SPACE . $sample_name_child;
+    push @commands, q{--reads_child} . $SPACE . $reads_child;
+    push @commands, q{--output_gvcf_child} . $SPACE . $output_gvcf_child;
+    push @commands, q{--output_vcf_child} . $SPACE . $output_vcf_child;
+
+    ## Parent1
+    push @commands, q{--sample_name_parent1} . $SPACE . $sample_name_parent1;
+    push @commands, q{--reads_parent1} . $SPACE . $reads_parent1;
+    push @commands, q{--output_gvcf_parent1} . $SPACE . $output_gvcf_parent1;
+    push @commands, q{--output_vcf_parent1} . $SPACE . $output_vcf_parent1;
+
+    if ($sample_name_parent2) {
+        push @commands, q{--sample_name_parent2} . $SPACE . $sample_name_parent2;
+    }
+    if ($reads_parent2) {
+        push @commands, q{--reads_parent2} . $SPACE . $reads_parent2;
+    }
+    if ($output_gvcf_parent2) {
+        push @commands, q{--output_gvcf_parent2} . $SPACE . $output_gvcf_parent2;
+    }
+    if ($output_vcf_parent2) {
+        push @commands, q{--output_vcf_parent2} . $SPACE . $output_vcf_parent2;
+    }
+    if ($bedfile) {
+        push @commands, q{--regions} . $SPACE . $bedfile;
+    }
+
+    push @commands,
+      unix_standard_streams(
+        {
+            stderrfile_path        => $stderrfile_path,
+            stderrfile_path_append => $stderrfile_path_append,
+            stdinfile_path         => $stdinfile_path,
+            stdoutfile_path        => $stdoutfile_path,
+        }
+      );
+
+    unix_write_to_file(
+        {
+            commands_ref => \@commands,
+            filehandle   => $filehandle,
+            separator    => $SPACE,
+
+        }
+    );
+    return @commands;
+}
+
+1;
diff --git a/lib/MIP/Recipes/Analysis/Deeptrio.pm b/lib/MIP/Recipes/Analysis/Deeptrio.pm
new file mode 100644
index 000000000..edd63feae
--- /dev/null
+++ b/lib/MIP/Recipes/Analysis/Deeptrio.pm
@@ -0,0 +1,324 @@
+package MIP::Recipes::Analysis::Deeptrio;
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Spec::Functions qw{ catdir catfile };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use utf8;
+use warnings;
+use warnings qw{ FATAL utf8 };
+
+## MIPs lib/
+use MIP::Constants qw{ $LOG_NAME $NEWLINE $UNDERSCORE };
+
+BEGIN {
+
+    require Exporter;
+    use base qw{ Exporter };
+
+    # Functions and variables which can be optionally exported
+    our @EXPORT_OK = qw{ analysis_deeptrio };
+
+}
+
+sub analysis_deeptrio {
+
+## Function : Returns vcfs and gvcfs from bam files using DeepVariant's deeptrio caller
+## Returns  :
+## Arguments: $active_parameter_href => Active parameters for this analysis hash {REF}
+##          : $case_id               => Family id
+##          : $file_info_href        => File_info hash {REF}
+##          : $job_id_href           => Job id hash {REF}
+##          : $parameter_href        => Parameter hash {REF}
+##          : $profile_base_command  => Submission profile base command
+##          : $recipe_name           => Recipe name
+##          : $sample_info_href      => Info on samples and case hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $active_parameter_href;
+    my $file_info_href;
+    my $job_id_href;
+    my $parameter_href;
+    my $recipe_name;
+    my $sample_info_href;
+
+    ## Default(s)
+    my $case_id;
+    my $profile_base_command;
+
+    my $tmpl = {
+        active_parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$active_parameter_href,
+            strict_type => 1,
+        },
+        case_id => {
+            default     => $arg_href->{active_parameter_href}{case_id},
+            store       => \$case_id,
+            strict_type => 1,
+        },
+        file_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$file_info_href,
+            strict_type => 1,
+        },
+        job_id_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$job_id_href,
+            strict_type => 1,
+        },
+        parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$parameter_href,
+            strict_type => 1,
+        },
+        profile_base_command => {
+            default     => q{sbatch},
+            store       => \$profile_base_command,
+            strict_type => 1,
+        },
+        recipe_name => {
+            defined     => 1,
+            required    => 1,
+            store       => \$recipe_name,
+            strict_type => 1,
+        },
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Get::File qw{ get_io_files };
+    use MIP::Get::Parameter qw{ get_recipe_attributes get_recipe_resources };
+    use MIP::Parse::File qw{ parse_io_outfiles };
+    use MIP::Processmanagement::Processes qw{ submit_recipe };
+    use MIP::Program::Deeptrio qw{ deeptrio };
+    use MIP::Program::Gnu::Coreutils qw{ gnu_mkdir };
+    use MIP::Sample_info
+      qw{ get_case_members_attributes_in_duos get_family_member_id set_recipe_metafile_in_sample_info set_recipe_outfile_in_sample_info };
+    use MIP::Script::Setup_script qw{ setup_script };
+
+    ### PREPROCESSING:
+
+    ## Retrieve logger object
+    my $log = Log::Log4perl->get_logger($LOG_NAME);
+
+    my %case_members_id =
+      scalar @{ $active_parameter_href->{sample_ids} } == 2
+      ? get_case_members_attributes_in_duos( { sample_info_href => $sample_info_href } )
+      : get_family_member_id( { sample_info_href => $sample_info_href } );
+
+    ## Unpack parameters
+    my $job_id_chain = get_recipe_attributes(
+        {
+            attribute      => q{chain},
+            parameter_href => $parameter_href,
+            recipe_name    => $recipe_name,
+        }
+    );
+
+    my $model_type = _consensus_analysis_type(
+        {
+            parameter_href => $parameter_href,
+        }
+    );
+
+    my $recipe_mode     = $active_parameter_href->{$recipe_name};
+    my %recipe_resource = get_recipe_resources(
+        {
+            active_parameter_href => $active_parameter_href,
+            recipe_name           => $recipe_name,
+        }
+    );
+
+    my $infile_name_prefix;
+
+    my @parents          = grep { defined } @{ \%case_members_id }{qw{ father mother }};
+    my @parents_filtered = grep { $_ ne '0' } @parents;
+    my $child_id         = $case_members_id{children}[0];
+
+    my %iofile_parameter;
+    my @outfile_directories;
+
+  SAMPLE_ID:
+    foreach my $sample_id ( @parents_filtered, $child_id ) {
+        my %sample_bam_io = get_io_files(
+            {
+                id             => $sample_id,
+                file_info_href => $file_info_href,
+                parameter_href => $parameter_href,
+                recipe_name    => q{markduplicates},
+                stream         => q{out},
+            }
+        );
+        $infile_name_prefix = $sample_bam_io{in}{file_name_prefix};
+
+        my %sample_vcf_io = (
+            %sample_bam_io,
+            parse_io_outfiles(
+                {
+                    chain_id               => $job_id_chain,
+                    id                     => $sample_id,
+                    file_info_href         => $file_info_href,
+                    file_name_prefixes_ref => [$infile_name_prefix],
+                    outdata_dir            => $active_parameter_href->{outdata_dir},
+                    parameter_href         => $parameter_href,
+                    recipe_name            => $recipe_name,
+                }
+            )
+        );
+        $iofile_parameter{$sample_id}{reads} =
+          $sample_bam_io{out}{file_path_prefix} . $sample_bam_io{out}{file_suffix};
+        $iofile_parameter{$sample_id}{output_gvcf} = $sample_vcf_io{out}{file_path};
+        $iofile_parameter{$sample_id}{output_vcf} =
+          $sample_vcf_io{out}{file_path_prefix} . q{.vcf.gz};
+        $iofile_parameter{$sample_id}{sample_name} = $sample_id;
+        push @outfile_directories, $sample_vcf_io{out}{dir_path};
+    }
+
+    ## Filehandles
+    # Create anonymous filehandle
+    my $filehandle = IO::Handle->new();
+
+    ## Creates recipe directories (info & data & script), recipe script filenames and writes sbatch header
+    my ( $recipe_file_path, $recipe_info_path ) = setup_script(
+        {
+            active_parameter_href => $active_parameter_href,
+            core_number           => $recipe_resource{core_number},
+            directory_id          => $case_id,
+            filehandle            => $filehandle,
+            gpu_number            => $recipe_resource{gpu_number},
+            job_id_href           => $job_id_href,
+            memory_allocation     => $recipe_resource{memory},
+            process_time          => $recipe_resource{time},
+            recipe_directory      => $recipe_name,
+            recipe_name           => $recipe_name,
+        }
+    );
+
+    ### SHELL:
+
+    say {$filehandle} q{## Create output directories};
+    foreach my $out_directory (@outfile_directories) {
+        gnu_mkdir(
+            {
+                filehandle       => $filehandle,
+                indirectory_path => $out_directory,
+                parents          => 1,
+            }
+        );
+        say {$filehandle} $NEWLINE;
+    }
+
+    say {$filehandle} q{## } . $recipe_name;
+    deeptrio(
+        {
+            filehandle          => $filehandle,
+            model_type          => $model_type,
+            num_shards          => $recipe_resource{core_number},
+            output_gvcf_child   => $iofile_parameter{$child_id}{output_gvcf},
+            output_gvcf_parent1 => $iofile_parameter{ $parents[0] }{output_gvcf},
+            output_gvcf_parent2 => $iofile_parameter{ $parents[1] }{output_gvcf},
+            output_vcf_child    => $iofile_parameter{$child_id}{output_vcf},
+            output_vcf_parent1  => $iofile_parameter{ $parents[0] }{output_vcf},
+            output_vcf_parent2  => $iofile_parameter{ $parents[1] }{output_vcf},
+            referencefile_path  => $active_parameter_href->{human_genome_reference},
+            reads_child         => $iofile_parameter{$child_id}{reads},
+            reads_parent1       => $iofile_parameter{ $parents[0] }{reads},
+            reads_parent2       => $iofile_parameter{ $parents[1] }{reads},
+            sample_name_child   => $iofile_parameter{$child_id}{sample_name},
+            sample_name_parent1 => $iofile_parameter{ $parents[0] }{sample_name},
+            sample_name_parent2 => $iofile_parameter{ $parents[1] }{sample_name},
+        }
+    );
+
+    ## Close filehandleS
+    close $filehandle or $log->logcroak(q{Could not close filehandle});
+
+    if ( $recipe_mode == 1 ) {
+
+        ## Collect QC metadata info for later use
+        set_recipe_outfile_in_sample_info(
+            {
+                infile           => $iofile_parameter{$child_id}{output_gvcf},
+                recipe_name      => $recipe_name,
+                sample_info_href => $sample_info_href,
+            }
+        );
+
+        submit_recipe(
+            {
+                base_command                      => $profile_base_command,
+                case_id                           => $case_id,
+                dependency_method                 => q{sample_to_case},
+                job_id_chain                      => $job_id_chain,
+                job_id_href                       => $job_id_href,
+                job_reservation_name              => $active_parameter_href->{job_reservation_name},
+                log                               => $log,
+                max_parallel_processes_count_href =>
+                  $file_info_href->{max_parallel_processes_count},
+                recipe_file_path   => $recipe_file_path,
+                sample_ids_ref     => \@{ $active_parameter_href->{sample_ids} },
+                submission_profile => $active_parameter_href->{submission_profile},
+            }
+        );
+    }
+    return 1;
+}
+
+sub _consensus_analysis_type {
+
+## Function : Determine model type from consensus analysis type
+## Returns  :
+## Arguments: $parameter_href => Parameter hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $parameter_href;
+
+    my $tmpl = {
+        parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$parameter_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Parameter qw{ get_cache };
+
+    my %deepvar_consensus_analysis_type_map =
+      ( MIXED => q{WGS}, PANEL => q{WES}, WGS => q{WGS}, WES => q{WES} );
+    my $consensus_analysis_type = get_cache(
+        {
+            parameter_href => $parameter_href,
+            parameter_name => q{consensus_analysis_type},
+        }
+    );
+    return $deepvar_consensus_analysis_type_map{ uc $consensus_analysis_type };
+}
+
+1;
diff --git a/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm b/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm
index 898c14506..817c5a5d0 100644
--- a/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm
+++ b/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm
@@ -117,8 +117,7 @@ sub parse_rd_dna {
     use MIP::Gatk qw{ check_gatk_sample_map_paths };
     use MIP::Parameter qw{ get_cache };
     use MIP::Parse::Gender qw{ parse_fastq_for_gender };
-    use MIP::Reference
-      qw{ get_select_file_contigs parse_exome_target_bed parse_nist_parameters };
+    use MIP::Reference qw{ get_select_file_contigs parse_exome_target_bed parse_nist_parameters };
     use MIP::Sample_info qw{ set_parameter_in_sample_info };
     use MIP::Vep qw{
       check_vep_api_cache_versions
@@ -127,11 +126,9 @@ sub parse_rd_dna {
     use MIP::Vcfanno qw{ parse_toml_config_parameters };
 
     ## Constants
-    Readonly my @MIP_VEP_PLUGINS => qw{ sv_vep_plugin vep_plugin };
-    Readonly my @ONLY_WGS_VARIANT_CALLER_RECIPES =>
-      qw{ cnvnator_ar delly_reformat tiddit };
-    Readonly my @ONLY_WGS_RECIPIES =>
-      qw{ cnvnator_ar delly_call delly_reformat expansionhunter
+    Readonly my @MIP_VEP_PLUGINS                 => qw{ sv_vep_plugin vep_plugin };
+    Readonly my @ONLY_WGS_VARIANT_CALLER_RECIPES => qw{ cnvnator_ar delly_reformat tiddit };
+    Readonly my @ONLY_WGS_RECIPIES => qw{ cnvnator_ar delly_call delly_reformat expansionhunter
       samtools_subsample_mt smncopynumbercaller star_caller telomerecat_ar tiddit };
     Readonly my @REMOVE_CONFIG_KEYS => qw{ associated_recipe };
 
@@ -155,11 +152,9 @@ sub parse_rd_dna {
     ## Update exome_target_bed files with human_genome_reference_source and human_genome_reference_version
     parse_exome_target_bed(
         {
-            exome_target_bed_file_href => $active_parameter_href->{exome_target_bed},
-            human_genome_reference_source =>
-              $file_info_href->{human_genome_reference_source},
-            human_genome_reference_version =>
-              $file_info_href->{human_genome_reference_version},
+            exome_target_bed_file_href     => $active_parameter_href->{exome_target_bed},
+            human_genome_reference_source  => $file_info_href->{human_genome_reference_source},
+            human_genome_reference_version => $file_info_href->{human_genome_reference_version},
         }
     );
 
@@ -442,7 +437,7 @@ sub pipeline_analyse_rd_dna {
     use MIP::Log::MIP_log4perl qw{ log_display_recipe_for_user };
     use MIP::Parse::Reference qw{ parse_references };
     use MIP::Set::Analysis
-      qw{ set_recipe_bwa_mem set_recipe_gatk_variantrecalibration set_recipe_on_analysis_type set_rankvariants_ar };
+      qw{ set_recipe_bwa_mem set_recipe_deepvariant set_recipe_gatk_variantrecalibration set_recipe_on_analysis_type set_rankvariants_ar };
 
     ## Recipes
     use MIP::Recipes::Analysis::Analysisrunstatus qw{ analysis_analysisrunstatus };
@@ -451,24 +446,22 @@ sub pipeline_analyse_rd_dna {
     use MIP::Recipes::Analysis::Chromograph
       qw{ analysis_chromograph_cov analysis_chromograph_rhoviz analysis_chromograph_upd };
     use MIP::Recipes::Analysis::Cnvnator qw{ analysis_cnvnator };
+    use MIP::Recipes::Analysis::Deeptrio qw { analysis_deeptrio };
     use MIP::Recipes::Analysis::Deepvariant qw { analysis_deepvariant };
     use MIP::Recipes::Analysis::Delly_call qw{ analysis_delly_call };
     use MIP::Recipes::Analysis::Delly_reformat qw{ analysis_delly_reformat };
-    use MIP::Recipes::Analysis::Endvariantannotationblock
-      qw{ analysis_endvariantannotationblock };
+    use MIP::Recipes::Analysis::Endvariantannotationblock qw{ analysis_endvariantannotationblock };
     use MIP::Recipes::Analysis::Expansionhunter qw{ analysis_expansionhunter };
     use MIP::Recipes::Analysis::Fastqc qw{ analysis_fastqc };
     use MIP::Recipes::Analysis::Frequency_filter qw{ analysis_frequency_filter };
-    use MIP::Recipes::Analysis::Gatk_baserecalibration
-      qw{ analysis_gatk_baserecalibration };
+    use MIP::Recipes::Analysis::Gatk_baserecalibration qw{ analysis_gatk_baserecalibration };
     use MIP::Recipes::Analysis::Gatk_combinevariantcallsets
       qw{ analysis_gatk_combinevariantcallsets };
     use MIP::Recipes::Analysis::Gatk_gathervcfs qw{ analysis_gatk_gathervcfs };
     use MIP::Recipes::Analysis::Gatk_genotypegvcfs qw{ analysis_gatk_genotypegvcfs };
     use MIP::Recipes::Analysis::Gatk_haplotypecaller qw{ analysis_gatk_haplotypecaller };
     use MIP::Recipes::Analysis::Gatk_variantevalall qw{ analysis_gatk_variantevalall };
-    use MIP::Recipes::Analysis::Gatk_variantevalexome
-      qw{ analysis_gatk_variantevalexome };
+    use MIP::Recipes::Analysis::Gatk_variantevalexome qw{ analysis_gatk_variantevalexome };
     use MIP::Recipes::Analysis::Glnexus qw{ analysis_glnexus };
     use MIP::Recipes::Analysis::Gzip_fastq qw{ analysis_gzip_fastq };
     use MIP::Recipes::Analysis::Manta qw{ analysis_manta };
@@ -487,21 +480,18 @@ sub pipeline_analyse_rd_dna {
       qw{ analysis_prepareforvariantannotationblock };
     use MIP::Recipes::Analysis::Rankvariant
       qw{ analysis_rankvariant analysis_rankvariant_unaffected analysis_rankvariant_sv analysis_rankvariant_sv_unaffected };
-    use MIP::Recipes::Analysis::Rhocall
-      qw{ analysis_rhocall_annotate analysis_rhocall_viz };
+    use MIP::Recipes::Analysis::Rhocall qw{ analysis_rhocall_annotate analysis_rhocall_viz };
     use MIP::Recipes::Analysis::Rtg_vcfeval qw{ analysis_rtg_vcfeval  };
     use MIP::Recipes::Analysis::Sacct qw{ analysis_sacct };
     use MIP::Recipes::Analysis::Sambamba_depth qw{ analysis_sambamba_depth };
     use MIP::Recipes::Analysis::Samtools_merge qw{ analysis_samtools_merge };
-    use MIP::Recipes::Analysis::Samtools_subsample_mt
-      qw{ analysis_samtools_subsample_mt };
+    use MIP::Recipes::Analysis::Samtools_subsample_mt qw{ analysis_samtools_subsample_mt };
     use MIP::Recipes::Analysis::Smncopynumbercaller qw{ analysis_smncopynumbercaller };
     use MIP::Recipes::Analysis::Split_fastq_file qw{ analysis_split_fastq_file };
     use MIP::Recipes::Analysis::Star_caller qw{ analysis_star_caller };
     use MIP::Recipes::Analysis::Sv_annotate qw{ analysis_sv_annotate };
     use MIP::Recipes::Analysis::Sv_reformat qw{ analysis_reformat_sv };
-    use MIP::Recipes::Analysis::Sv_combinevariantcallsets
-      qw{ analysis_sv_combinevariantcallsets };
+    use MIP::Recipes::Analysis::Sv_combinevariantcallsets qw{ analysis_sv_combinevariantcallsets };
     use MIP::Recipes::Analysis::Split_fastq_file qw{ analysis_split_fastq_file };
     use MIP::Recipes::Analysis::Telomerecat qw{ analysis_telomerecat };
     use MIP::Recipes::Analysis::Tiddit qw{ analysis_tiddit };
@@ -562,9 +552,10 @@ sub pipeline_analyse_rd_dna {
         chromograph_rhoviz => \&analysis_chromograph_rhoviz,
         chromograph_upd    => \$sample_info_href->{has_trio}
         ? \&analysis_chromograph_upd
-        : undef,                                               # Depends on pedigree
+        : undef,                                                        # Depends on pedigree
         cnvnator_ar                 => \&analysis_cnvnator,
-        deepvariant                 => \&analysis_deepvariant,
+        deeptrio                    => undef,
+        deepvariant                 => undef,
         delly_call                  => \&analysis_delly_call,
         delly_reformat              => \&analysis_delly_reformat,
         endvariantannotationblock   => \&analysis_endvariantannotationblock,
@@ -578,48 +569,46 @@ sub pipeline_analyse_rd_dna {
         gatk_haplotypecaller        => \&analysis_gatk_haplotypecaller,
         gatk_variantevalall         => \&analysis_gatk_variantevalall,
         gatk_variantevalexome       => \&analysis_gatk_variantevalexome,
-        gatk_variantrecalibration =>
-          undef,    # Depends on analysis type and/or number of samples
-        glnexus_merge                => \&analysis_glnexus,
-        gzip_fastq                   => \&analysis_gzip_fastq,
-        manta                        => \&analysis_manta,
-        markduplicates               => \&analysis_markduplicates,
-        multiqc_ar                   => \&analysis_multiqc,
-        peddy_ar                     => \&analysis_peddy,
-        picardtools_collecthsmetrics => \&analysis_picardtools_collecthsmetrics,
-        picardtools_collectmultiplemetrics =>
-          \&analysis_picardtools_collectmultiplemetrics,
-        plink                            => \&analysis_plink,
-        prepareforvariantannotationblock => \&analysis_prepareforvariantannotationblock,
-        qccollect_ar                     => \&analysis_mip_qccollect,
-        rankvariant    => undef,                         # Depends on sample features
-        rhocall_ar     => \&analysis_rhocall_annotate,
-        rhocall_viz    => \&analysis_rhocall_viz,
-        rtg_vcfeval    => \&analysis_rtg_vcfeval,
-        sacct          => \&analysis_sacct,
-        sambamba_depth => \&analysis_sambamba_depth,
-        samtools_merge => \&analysis_samtools_merge,
+        gatk_variantrecalibration   => undef,    # Depends on analysis type and/or number of samples
+        glnexus_merge                      => \&analysis_glnexus,
+        gzip_fastq                         => \&analysis_gzip_fastq,
+        manta                              => \&analysis_manta,
+        markduplicates                     => \&analysis_markduplicates,
+        multiqc_ar                         => \&analysis_multiqc,
+        peddy_ar                           => \&analysis_peddy,
+        picardtools_collecthsmetrics       => \&analysis_picardtools_collecthsmetrics,
+        picardtools_collectmultiplemetrics => \&analysis_picardtools_collectmultiplemetrics,
+        plink                              => \&analysis_plink,
+        prepareforvariantannotationblock   => \&analysis_prepareforvariantannotationblock,
+        qccollect_ar                       => \&analysis_mip_qccollect,
+        rankvariant               => undef,                             # Depends on sample features
+        rhocall_ar                => \&analysis_rhocall_annotate,
+        rhocall_viz               => \&analysis_rhocall_viz,
+        rtg_vcfeval               => \&analysis_rtg_vcfeval,
+        sacct                     => \&analysis_sacct,
+        sambamba_depth            => \&analysis_sambamba_depth,
+        samtools_merge            => \&analysis_samtools_merge,
         samtools_subsample_mt     => \&analysis_samtools_subsample_mt,
         smncopynumbercaller       => \&analysis_smncopynumbercaller,
         split_fastq_file          => \&analysis_split_fastq_file,
         star_caller               => \&analysis_star_caller,
         sv_annotate               => \&analysis_sv_annotate,
         sv_combinevariantcallsets => \&analysis_sv_combinevariantcallsets,
-        sv_rankvariant            => undef,                   # Depends on sample features
+        sv_rankvariant            => undef,                             # Depends on sample features
         sv_reformat               => \&analysis_reformat_sv,
-        sv_varianteffectpredictor => undef,                   # Depends on analysis type
-        sv_vcfparser              => undef,                   # Depends on analysis type
+        sv_varianteffectpredictor => undef,                             # Depends on analysis type
+        sv_vcfparser              => undef,                             # Depends on analysis type
         telomerecat_ar            => \&analysis_telomerecat,
         tiddit                    => \&analysis_tiddit,
-        tiddit_coverage        => \&analysis_tiddit_coverage,
-        upd_ar                 => $sample_info_href->{has_trio} ? \&analysis_upd : undef,
-        varg_ar                => \&analysis_varg,
-        varianteffectpredictor => \&analysis_vep_wgs,
-        variant_annotation     => \&analysis_variant_annotation,
-        version_collect_ar     => \&analysis_mip_vercollect,
-        vcfparser_ar           => \&analysis_mip_vcfparser,
-        vcf2cytosure_ar        => \&analysis_vcf2cytosure,
-        vt_ar                  => \&analysis_vt,
+        tiddit_coverage           => \&analysis_tiddit_coverage,
+        upd_ar                    => $sample_info_href->{has_trio} ? \&analysis_upd : undef,
+        varg_ar                   => \&analysis_varg,
+        varianteffectpredictor    => \&analysis_vep_wgs,
+        variant_annotation        => \&analysis_variant_annotation,
+        version_collect_ar        => \&analysis_mip_vercollect,
+        vcfparser_ar              => \&analysis_mip_vcfparser,
+        vcf2cytosure_ar           => \&analysis_vcf2cytosure,
+        vt_ar                     => \&analysis_vt,
     );
 
     ## Special case for rankvariants recipe
@@ -642,10 +631,17 @@ sub pipeline_analyse_rd_dna {
 
     ## Set correct bwa_mem recipe depending on version and source of the human_genome_reference: Source (hg19 or grch)
     set_recipe_bwa_mem(
+        {
+            analysis_recipe_href           => \%analysis_recipe,
+            human_genome_reference_version => $file_info_href->{human_genome_reference_version},
+        }
+    );
+
+    ## Set deepvariant or deeptrio recipe depending on the presence of parent-child duo or a trio
+    set_recipe_deepvariant(
         {
             analysis_recipe_href => \%analysis_recipe,
-            human_genome_reference_version =>
-              $file_info_href->{human_genome_reference_version},
+            sample_info_href     => $sample_info_href,
         }
     );
 
diff --git a/lib/MIP/Sample_info.pm b/lib/MIP/Sample_info.pm
index 45cd58ae8..8a62bd291 100644
--- a/lib/MIP/Sample_info.pm
+++ b/lib/MIP/Sample_info.pm
@@ -27,6 +27,7 @@ BEGIN {
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
+      get_case_members_attributes_in_duos
       get_family_member_id
       get_read_group
       get_rg_header_line
@@ -52,6 +53,62 @@ BEGIN {
 
 }
 
+sub get_case_members_attributes_in_duos {
+
+## Function : Get the sample IDs and phenotypes of the family members
+## Returns  : %case_members_attributes
+## Arguments: $sample_info_href => Sample info hash {REF}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $sample_info_href;
+
+    my $tmpl = {
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my %case_members_attributes = (
+        affected => [],
+        children => [],
+        father   => 0,
+        mother   => 0,
+        unknown  => [],
+    );
+
+  SAMPLE_ID:
+    foreach my $sample_id ( keys %{ $sample_info_href->{sample} } ) {
+
+        my %sample_attributes = get_pedigree_sample_id_attributes(
+            {
+                sample_id        => $sample_id,
+                sample_info_href => $sample_info_href,
+            }
+        );
+
+        my $phenotype = $sample_attributes{phenotype};
+        push @{ $case_members_attributes{$phenotype} }, $sample_id;
+
+        next SAMPLE_ID if ( not( $sample_attributes{father} or $sample_attributes{mother} ) );
+
+        ## Append child
+        push @{ $case_members_attributes{children} }, $sample_id;
+
+        $case_members_attributes{father} = $sample_attributes{father};
+        $case_members_attributes{mother} = $sample_attributes{mother};
+    }
+
+    return %case_members_attributes;
+}
+
 sub get_family_member_id {
 
 ## Function : Get the sample IDs of the family members
@@ -1525,7 +1582,7 @@ sub set_parameter_in_sample_info {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    use MIP::Pedigree qw{ has_trio };
+    use MIP::Pedigree qw{ has_duo has_trio };
 
     my %set_parameter_map = (
         analysis_type => {
@@ -1538,6 +1595,16 @@ sub set_parameter_in_sample_info {
             set_at => $sample_info_href,
             value  => $active_parameter_href->{expected_coverage},
         },
+        has_duo => {
+            key    => q{has_duo},
+            set_at => $sample_info_href,
+            value  => has_duo(
+                {
+                    active_parameter_href => $active_parameter_href,
+                    sample_info_href      => $sample_info_href,
+                }
+            ),
+        },
         has_trio => {
             key    => q{has_trio},
             set_at => $sample_info_href,
diff --git a/lib/MIP/Set/Analysis.pm b/lib/MIP/Set/Analysis.pm
index 88e265fb6..1bdd5b275 100644
--- a/lib/MIP/Set/Analysis.pm
+++ b/lib/MIP/Set/Analysis.pm
@@ -25,6 +25,7 @@ BEGIN {
     our @EXPORT_OK = qw{
       set_rankvariants_ar
       set_recipe_bwa_mem
+      set_recipe_deepvariant
       set_recipe_gatk_variantrecalibration
       set_recipe_on_analysis_type
       set_recipe_star_aln
@@ -78,6 +79,56 @@ sub set_recipe_bwa_mem {
     return;
 }
 
+sub set_recipe_deepvariant {
+
+## Function : Set deeptrio or deepvariant recipe depending on the presence of parent-child duo or trio
+## Returns  :
+## Arguments: $analysis_recipe_href => Analysis recipe hash {REF}
+##          : $sample_info_href     => Sample info hash {HASH}
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $analysis_recipe_href;
+    my $sample_info_href;
+
+    my $tmpl = {
+        analysis_recipe_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$analysis_recipe_href,
+            strict_type => 1,
+        },
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Recipes::Analysis::Deepvariant qw{ analysis_deepvariant };
+    use MIP::Recipes::Analysis::Deeptrio qw{ analysis_deeptrio };
+
+    $analysis_recipe_href->{deepvariant} = \&analysis_deepvariant;
+    $analysis_recipe_href->{deeptrio}    = undef;
+
+  CONSTELLATION_STATE:
+    foreach my $constellation_state (qw{ has_duo has_trio }) {
+
+        next CONSTELLATION_STATE if ( not $sample_info_href->{$constellation_state} );
+
+        $analysis_recipe_href->{deepvariant} = undef;
+        $analysis_recipe_href->{deeptrio}    = \&analysis_deeptrio;
+        return;
+    }
+    return;
+}
+
 sub set_recipe_gatk_variantrecalibration {
 
 ## Function : Update which gatk variant recalibration to use depending on number of samples
diff --git a/t/analysis_deeptrio.t b/t/analysis_deeptrio.t
new file mode 100644
index 000000000..c8cb086e3
--- /dev/null
+++ b/t/analysis_deeptrio.t
@@ -0,0 +1,136 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir catfile };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2018 };
+use Test::Trap;
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COLON $COMMA $SPACE };
+use MIP::Test::Fixtures qw{ test_add_io_for_recipe test_log test_mip_hashes };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::Recipes::Analysis::Deepvariant} => [qw{ analysis_deepvariant }],
+        q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Recipes::Analysis::Deeptrio qw{ analysis_deeptrio };
+
+diag(   q{Test analysis_deeptrio from Deeptrio.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+my $log = test_log( { log_name => q{MIP}, no_screen => 1, } );
+
+## Given analysis parameters
+my $recipe_name    = q{deeptrio};
+my $slurm_mock_cmd = catfile( $Bin, qw{ data modules slurm-mock.pl } );
+
+my %active_parameter = test_mip_hashes(
+    {
+        mip_hash_name => q{active_parameter},
+        recipe_name   => $recipe_name,
+    }
+);
+
+$active_parameter{$recipe_name}                     = 1;
+$active_parameter{recipe_core_number}{$recipe_name} = 1;
+$active_parameter{recipe_gpu_number}{$recipe_name}  = 1;
+$active_parameter{recipe_time}{$recipe_name}        = 1;
+
+my $case_id = $active_parameter{case_id};
+
+my %file_info = test_mip_hashes(
+    {
+        mip_hash_name => q{file_info},
+        recipe_name   => $recipe_name,
+    }
+);
+
+my %job_id;
+my %parameter = test_mip_hashes(
+    {
+        mip_hash_name => q{recipe_parameter},
+        recipe_name   => $recipe_name,
+    }
+);
+
+my @order_recipes = ( qw{ markduplicates }, $recipe_name );
+
+SAMPLE_ID:
+foreach my $sample_id ( @{ $active_parameter{sample_ids} } ) {
+
+    test_add_io_for_recipe(
+        {
+            file_info_href => \%file_info,
+            id             => $sample_id,
+            parameter_href => \%parameter,
+            recipe_name    => q{markduplicates},
+            step           => q{bam},
+        }
+    );
+    test_add_io_for_recipe(
+        {
+            file_info_href    => \%file_info,
+            id                => $sample_id,
+            order_recipes_ref => \@order_recipes,
+            parameter_href    => \%parameter,
+            recipe_name       => $recipe_name,
+            step              => q{vcf},
+        }
+    );
+}
+
+$parameter{cache}{consensus_analysis_type} = q{WGS};
+
+my %sample_info = test_mip_hashes(
+    {
+        mip_hash_name => q{qc_sample_info},
+        recipe_name   => $recipe_name,
+    }
+);
+
+my $is_ok = analysis_deeptrio(
+    {
+        active_parameter_href => \%active_parameter,
+        case_id               => $case_id,
+        file_info_href        => \%file_info,
+        job_id_href           => \%job_id,
+        parameter_href        => \%parameter,
+        profile_base_command  => $slurm_mock_cmd,
+        recipe_name           => $recipe_name,
+        sample_info_href      => \%sample_info,
+    }
+);
+
+## Then return TRUE
+ok( $is_ok, q{ Executed analysis recipe } . $recipe_name );
+
+done_testing();
diff --git a/t/deeptrio.t b/t/deeptrio.t
new file mode 100644
index 000000000..5fa96e6c3
--- /dev/null
+++ b/t/deeptrio.t
@@ -0,0 +1,163 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir catfile };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Commands qw{ test_function };
+
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::Program::Deeptrio} => [qw{ deeptrio }],
+);
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Program::Deeptrio qw{ deeptrio };
+
+diag(   q{Test deeptrio from Deeptrio.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Base arguments
+my @function_base_commands = qw{ run_deeptrio };
+
+my %base_argument = (
+    filehandle => {
+        input           => undef,
+        expected_output => \@function_base_commands,
+    },
+    stderrfile_path => {
+        input           => q{stderrfile.test},
+        expected_output => q{2> stderrfile.test},
+    },
+    stderrfile_path_append => {
+        input           => q{stderrfile.test},
+        expected_output => q{2>> stderrfile.test},
+    },
+    stdoutfile_path => {
+        input           => q{stdoutfile.test},
+        expected_output => q{1> stdoutfile.test},
+    },
+);
+
+## Can be duplicated with %base_argument and/or %specific_argument
+## to enable testing of each individual argument
+my %required_argument = (
+    model_type          => {
+        input           => q{WES},
+        expected_output => q{--model_type WES},
+    },
+    num_shards          => {
+        input           => q{36},
+        expected_output => q{--num_shards 36},
+    },
+    output_gvcf_child   => {
+        input           => catfile(q{ dir outfile.g.vcf }),
+        expected_output => q{--output_gvcf_child } . catfile(q{ dir outfile.g.vcf }),
+    },
+    output_gvcf_parent1 => {
+        input           => catfile(q{ dir outfile.g.vcf }),
+        expected_output => q{--output_gvcf_parent1 } . catfile(q{ dir outfile.g.vcf }),
+    },
+    output_vcf_child    => {
+        input           => catfile(q{ dir outfile.vcf }),
+        expected_output => q{--output_vcf_child } . catfile(q{ dir outfile.vcf }),
+    },
+    output_vcf_parent1  => {
+        input           => catfile(q{ dir outfile.vcf }),
+        expected_output => q{--output_vcf_parent1 }  . catfile(q{ dir outfile.vcf }),
+    },
+    reads_child         => {
+        input           => catfile(qw{ dir infile.bam }),
+        expected_output => q{--reads_child } . catfile(qw{ dir infile.bam }) ,
+    },
+    reads_parent1       => {
+        input           => catfile(qw{ dir infile.bam }),
+        expected_output => q{--reads_parent1 } . catfile(qw{ dir infile.bam }),
+    },
+    referencefile_path  => {
+        input           => q{test},
+        expected_output => q{--ref test},
+    },
+    sample_name_child   => {
+        input           => q{child},
+        expected_output => q{--sample_name_child } . q{child},
+    },
+    sample_name_parent1 => {
+        input           => q{father},
+        expected_output => q{--sample_name_parent1 } . q{father},
+    },
+);
+
+my %specific_argument = (
+    bedfile => {
+        input           => catfile(qw{ dir infile.bed }),
+        expected_output => q{--regions } . catfile(qw{ dir infile.bed }),
+    },
+    output_gvcf_parent2 => {
+        input           => catfile(q{ dir outfile.g.vcf }),
+        expected_output => q{--output_gvcf_parent2 } . catfile(q{ dir outfile.g.vcf }),
+    },
+    output_vcf_parent2  => {
+        input => catfile(q{ dir outfile.vcf }),
+        expected_output => q{--output_vcf_parent2 }  . catfile(q{ dir outfile.vcf }),
+    },
+    reads_parent2 => {
+        input           => catfile(qw{ dir infile.bam }),
+        expected_output => q{--reads_parent2 } . catfile(qw{ dir infile.bam }),
+    },
+    sample_name_parent2 => {
+        input => q{mother},
+        expected_output => q{--sample_name_parent2 } . q{mother},
+    },
+);
+
+## Coderef - enables generalized use of generate call
+my $module_function_cref = \&deeptrio;
+
+## Test both base and function specific arguments
+my @arguments = ( \%base_argument, \%specific_argument );
+
+ARGUMENT_HASH_REF:
+foreach my $argument_href (@arguments) {
+
+    my @commands = test_function(
+        {
+            argument_href              => $argument_href,
+            do_test_base_command       => 1,
+            function_base_commands_ref => \@function_base_commands,
+            module_function_cref       => $module_function_cref,
+            required_argument_href     => \%required_argument,
+        }
+    );
+}
+
+done_testing();
diff --git a/t/get_case_members_attributes_in_duos.t b/t/get_case_members_attributes_in_duos.t
new file mode 100644
index 000000000..d4278a2c6
--- /dev/null
+++ b/t/get_case_members_attributes_in_duos.t
@@ -0,0 +1,69 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Fixtures qw{ test_mip_hashes };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::Sample_info}    => [qw{ get_case_members_attributes_in_duos }],
+        q{MIP::Test::Fixtures} => [qw{ test_mip_hashes }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Sample_info qw{ get_case_members_attributes_in_duos };
+
+diag(   q{Test get_case_members_attributes_in_duos from Sample_info.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Given sample_info hash
+my %sample_info = test_mip_hashes( { mip_hash_name => q{qc_sample_info}, } );
+$sample_info{sample}{ADM1059A2}{phenotype} = q{unknown};
+$sample_info{sample}{ADM1059A1}{mother}    = q{0};
+
+delete $sample_info{sample}{ADM1059A3};
+my %family_member_id =
+  get_case_members_attributes_in_duos( { sample_info_href => \%sample_info, } );
+
+## Then return family members id
+my %expected = (
+    affected => [qw{ ADM1059A1 }],
+    children => [qw{ ADM1059A1 }],
+    father   => q{ADM1059A2},
+    mother   => q{0},
+    unknown  => [qw{ ADM1059A2 }],
+);
+
+is_deeply( \%family_member_id, \%expected, q{Got family hash} );
+
+done_testing();
diff --git a/t/has_duo.t b/t/has_duo.t
new file mode 100644
index 000000000..884f82e8b
--- /dev/null
+++ b/t/has_duo.t
@@ -0,0 +1,105 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Fixtures qw{ test_mip_hashes };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::Pedigree}       => [qw{ has_duo }],
+        q{MIP::Test::Fixtures} => [qw{ test_mip_hashes }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Pedigree qw{ has_duo };
+
+diag(   q{Test has_duo from Pedigre.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+my %active_parameter = test_mip_hashes( { mip_hash_name => q{active_parameter}, } );
+my %sample_info      = test_mip_hashes( { mip_hash_name => q{qc_sample_info}, } );
+
+## Given a trio where a sample id has phenotype affected
+
+## When checking if case constellation is duo and has samples with phenotype "affected"
+my $has_duo = has_duo(
+    {
+        active_parameter_href => \%active_parameter,
+        sample_info_href      => \%sample_info,
+    }
+);
+
+## Then return 0
+is( $has_duo, 0, q{Detected non duo constellation for trio} );
+
+## Given a duo where a sample id has phenotype affected
+@{ $active_parameter{sample_ids} } = (qw{ADM1059A1 ADM1059A2});
+
+## When checking if case constellation is duo and has samples with phenotype "affected"
+$has_duo = has_duo(
+    {
+        active_parameter_href => \%active_parameter,
+        sample_info_href      => \%sample_info,
+    }
+);
+
+## Then return 1
+ok( $has_duo, q{Detected duo constellation} );
+
+$sample_info{sample}{ADM1059A1}{phenotype} = q{unaffected};
+
+## When checking if case constellation is duo and has samples with phenotype "affected"
+$has_duo = has_duo(
+    {
+        active_parameter_href => \%active_parameter,
+        sample_info_href      => \%sample_info,
+    }
+);
+
+## Then return 0
+is( $has_duo, 0, q{Detected no samples with phenotype affected} );
+
+## Given a single sample case
+@{ $active_parameter{sample_ids} } = (q{ADM1059A1});
+
+## When checking if case constellation is duo and has samples with phenotype "affected"
+$has_duo = has_duo(
+    {
+        active_parameter_href => \%active_parameter,
+        sample_info_href      => \%sample_info,
+    }
+);
+## Then return 0
+is( $has_duo, 0, q{Detected non duo constellation for single sample} );
+
+done_testing();
diff --git a/t/set_parameter_in_sample_info.t b/t/set_parameter_in_sample_info.t
index 56d62ff77..e35f99d9a 100644
--- a/t/set_parameter_in_sample_info.t
+++ b/t/set_parameter_in_sample_info.t
@@ -90,9 +90,10 @@ my %expected_sample_info = (
 $expected_sample_info{analysis_type} = $active_parameter{analysis_type};
 %{ $expected_sample_info{expected_coverage} } = %{ $active_parameter{expected_coverage} };
 $expected_sample_info{pedigree_file}{path} = $active_parameter{pedigree_file};
-$expected_sample_info{log_file_dir} = dirname( dirname( $active_parameter{log_file} ) );
-$expected_sample_info{last_log_file_path} = $active_parameter{log_file};
-$expected_sample_info{has_trio}           = 0;
+$expected_sample_info{log_file_dir}        = dirname( dirname( $active_parameter{log_file} ) );
+$expected_sample_info{last_log_file_path}  = $active_parameter{log_file};
+$expected_sample_info{has_trio}            = 0;
+$expected_sample_info{has_duo}             = 0;
 
 ## Then these entries should be set in sample info
 is_deeply( \%sample_info, \%expected_sample_info, q{Set parameter in sample_info} );
diff --git a/t/set_recipe_deepvariant.t b/t/set_recipe_deepvariant.t
new file mode 100644
index 000000000..ffe18bc08
--- /dev/null
+++ b/t/set_recipe_deepvariant.t
@@ -0,0 +1,105 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::Recipes::Analysis::Deepvariant} => [qw{ analysis_deepvariant }],
+        q{MIP::Recipes::Analysis::Deeptrio}    => [qw{ analysis_deeptrio }],
+        q{MIP::Set::Analysis}                  => [qw{ set_recipe_deepvariant }],
+        q{MIP::Test::Fixtures}                 => [qw{ test_mip_hashes }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Set::Analysis qw{ set_recipe_deepvariant };
+use MIP::Recipes::Analysis::Deeptrio qw{ analysis_deeptrio };
+use MIP::Recipes::Analysis::Deepvariant qw{ analysis_deepvariant };
+use MIP::Test::Fixtures qw{ test_mip_hashes };
+
+diag(   q{Test set_recipe_deepvariant from Analysis.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+my %sample_info = test_mip_hashes( { mip_hash_name => q{qc_sample_info} } );
+my %analysis_recipe;
+
+## When constellation state is a duo
+$sample_info{has_duo}  = 1;
+$sample_info{has_trio} = 0;
+
+set_recipe_deepvariant(
+    {
+        analysis_recipe_href => \%analysis_recipe,
+        sample_info_href     => \%sample_info,
+    }
+);
+my %expected_analysis_recipe = (
+    deepvariant => undef,
+    deeptrio    => \&analysis_deeptrio,
+);
+
+## Then set deepvariant recipe
+is_deeply( \%analysis_recipe, \%expected_analysis_recipe, q{Set deepvariant recipe for a duo} );
+
+## When constellation state is a trio
+$sample_info{has_duo}  = 0;
+$sample_info{has_trio} = 1;
+set_recipe_deepvariant(
+    {
+        analysis_recipe_href => \%analysis_recipe,
+        sample_info_href     => \%sample_info,
+    }
+);
+$expected_analysis_recipe{deeptrio}    = \&analysis_deeptrio;
+$expected_analysis_recipe{deepvariant} = undef;
+
+## Then set deepvariant recipe
+is_deeply( \%analysis_recipe, \%expected_analysis_recipe, q{Set deepvariant recipe for a trio} );
+
+## When constellation state is neither a duo or trio
+$sample_info{has_duo}  = 0;
+$sample_info{has_trio} = 0;
+set_recipe_deepvariant(
+    {
+        analysis_recipe_href => \%analysis_recipe,
+        sample_info_href     => \%sample_info,
+    }
+);
+$expected_analysis_recipe{deeptrio}    = undef;
+$expected_analysis_recipe{deepvariant} = \&analysis_deepvariant;
+
+## Then set bwa mem recipe
+is_deeply( \%analysis_recipe, \%expected_analysis_recipe,
+    q{Set deepvariant recipe when the case is neither a duo or a trio} );
+
+done_testing();
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 6c24b48f9..584195743 100644
--- a/templates/mip_install_config.yaml
+++ b/templates/mip_install_config.yaml
@@ -68,7 +68,12 @@ container:
       call_variants: /opt/deepvariant/bin/call_variants
       postprocess_variants: /opt/deepvariant/bin/postprocess_variants
     gpu_support: 1
-    uri: docker.io/google/deepvariant:1.0.0-gpu
+    uri: docker.io/google/deepvariant:1.1.0-gpu
+  deeptrio:
+    executable:
+      run_deeptrio: /opt/deepvariant/bin/deeptrio/run_deeptrio
+    gpu_support: 1
+    uri: docker.io/google/deepvariant:deeptrio-1.1.0-gpu
   delly:
     executable:
       delly:
diff --git a/templates/program_test_cmds.yaml b/templates/program_test_cmds.yaml
index 9c8595564..9a9e524c1 100644
--- a/templates/program_test_cmds.yaml
+++ b/templates/program_test_cmds.yaml
@@ -32,6 +32,8 @@ cyrius:
   execution: 'star_caller.py --help'
 deepvariant:
   path: 'run_deepvariant'
+deeptrio:
+  path: 'run_deeptrio'
 delly:
   execution: 'delly'
 expansionhunter: