Merge f4ee825 into ec1d691

Clinical-Genomics · Jan 8, 2021 · e4022ea · e4022ea
2 parents ec1d691 + f4ee825
commit e4022ea
Show file tree

Hide file tree

Showing 18 changed files with 1,419 additions and 71 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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