Merge 0cb727e into 7980631

CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## Develop
+
+- Adds loqudb and gnomad frequencies to vcf2cytosure filtering
+- Store PCT_PF_READS_IMPROPER_PAIRS in qc file
+- Evaluate and fail analysis where PCT_PF_READS_IMPROPER_PAIRS is above 5 %
+
 ## [12.0.0]
 
 - Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default

definitions/rd_dna_parameters.yaml

@@ -1057,7 +1057,7 @@ vcf2cytosure_exclude_filter:
   associated_recipe:
     - vcf2cytosure_ar
   data_type: SCALAR
-  default: "'clingen_ngiAF > 0.1 || swegenAF > 0.05 || clinical_genomics_mipAF > 0.05 || decipherAF > 0.1'"
+  default: "'clingen_ngiAF > 0.1 || swegenAF > 0.05 || clinical_genomics_mipAF > 0.05 || decipherAF > 0.1 || clinical_genomics_loqusFrq > 0.05 || gnomad_svAF > 0.05'"
   type: recipe_argument
 vcf2cytosure_freq:
   associated_recipe:
@@ -1069,7 +1069,7 @@ vcf2cytosure_freq_tag:
   associated_recipe:
     - vcf2cytosure_ar
   data_type: SCALAR
-  default: FRQ
+  default: clinical_genomics_loqusFrq
   type: recipe_argument
 vcf2cytosure_maxbnd:
   associated_recipe:

lib/MIP/Main/Qccollect.pm

@@ -555,7 +555,7 @@ sub parse_limit_qc_output {
 
     return if not $limit_qc_output;
 
-    Readonly my @SKIP_QC_METRICS => qw{ collectmultiplemetrics variantevalall variantevalexome };
+    Readonly my @SKIP_QC_METRICS => qw{ variantevalall variantevalexome };
 
     foreach my $delete_metric_key (@SKIP_QC_METRICS) {
 

lib/MIP/Qccollect.pm

@@ -455,7 +455,7 @@ sub define_evaluate_metric {
 
 sub evaluate_analysis {
 
-## Function  : Read in aevaluate metrics and evaluate on sample and case level
+## Function  : Read in evaluation metrics and evaluate on sample and case level
 ## Returns   :
 ## Arguments : eval_metric_file  => File with evaluation metrics
 ##           : qc_data_href      => QC data {REF}
@@ -896,7 +896,6 @@ sub parse_sample_qc_metric {
                       $evaluate_metric_href->{$sample_id}{$recipe_name}{$metric},
                 }
             );
-            next METRIC;
         }
     }
     return 1;

lib/MIP/Store.pm

@@ -149,6 +149,10 @@ sub define_qc_metrics_to_store {
             analysis_mode => q{sample},
             recipe_name   => q{collecthsmetrics},
         },
+        PCT_PF_READS_IMPROPER_PAIRS => {
+            analysis_mode => q{sample},
+            recipe_name => q{collectmultiplemetrics},
+        },
         PCT_TARGET_BASES_10X => {
             analysis_mode => q{sample},
             recipe_name   => q{collecthsmetrics},

t/parse_limit_qc_output.t

@@ -47,7 +47,7 @@ my %qc_data = (
     sample => {
         sample_id => {
             recipe_output_file => {
-                collectmultiplemetrics => {
+                variantevalall => {
                     header => q{data},
                 },
             },
@@ -68,7 +68,7 @@ parse_limit_qc_output(
     }
 );
 
-## Then remove key collectmultiplemetrics
+## Then remove key variantevallall
 my %expected_qc_data = (
     sample => {
         sample_id => {

t/parse_sample_qc_metric.t

@@ -49,20 +49,20 @@ diag(   q{Test parse_sample_qc_metric from Qccollect.pm}
 
 ## Constants
 Readonly my $PCT_TARGET_BASES_10X         => 0.95;
+Readonly my $FAIL_PCT_TARGET_BASES_10X    => 0.90;
 Readonly my $PERCENTAGE_MAPPED_READS_EVAL => 95;
 Readonly my $PERCENTAGE_MAPPED_READS_PASS => 99;
 
 ## Given sample qc data when metric lacks a header
-my $infile    = q{an_infile};
-my $metric    = q{percentage_mapped_reads};
+my $infile        = q{an_infile};
+my $metric        = q{percentage_mapped_reads};
 my $header_recipe = q{collecthsmetrics};
 my $header_metric = q{PCT_TARGET_BASES_10X};
-my $recipe    = q{bamstats};
-my $sample_id = q{ADM1059A1};
-my %qc_data   = (
+my $recipe        = q{bamstats};
+my $sample_id     = q{ADM1059A1};
+my %qc_data       = (
     sample => {
-        $sample_id =>
-          { $infile => { $recipe => { $metric => $PERCENTAGE_MAPPED_READS_PASS }, }, },
+        $sample_id => { $infile => { $recipe => { $metric => $PERCENTAGE_MAPPED_READS_PASS }, }, },
     }
 );
 
@@ -104,9 +104,13 @@ my $is_ok = parse_sample_qc_metric(
 );
 ok( $is_ok, q{Parsed sample qc data metrics} );
 
-## Given sample qc data when metric has a header
-my $data_header   = q{first_of_pair};
-$qc_data{sample}{$sample_id}{$infile}{$header_recipe}{header}{$data_header}{$header_metric} = $PCT_TARGET_BASES_10X;
+## Given sample qc data when metric has headers
+my $data_header = q{first_of_pair};
+$qc_data{sample}{$sample_id}{$infile}{$header_recipe}{header}{$data_header}{$header_metric} =
+  $PCT_TARGET_BASES_10X;
+my $second_data_header = q{second_of_pair};
+$qc_data{sample}{$sample_id}{$infile}{$header_recipe}{header}{$second_data_header}{$header_metric}
+  = $FAIL_PCT_TARGET_BASES_10X;
 
 ## Alias
 my $qc_data_header_recipe_href =
@@ -121,6 +125,14 @@ $is_ok = parse_sample_qc_metric(
         sample_id            => $sample_id,
     }
 );
+
+## Then parses format OK...
 ok( $is_ok, q{Parsed sample qc data header metrics} );
 
+## ... and fails qc check for the second header
+my $failed_evaluation =
+  q{FAILED:collecthsmetrics_PCT_TARGET_BASES_10X:} . $FAIL_PCT_TARGET_BASES_10X;
+is( $qc_data{evaluation}{collecthsmetrics}[0],
+    $failed_evaluation, q{Fails qc on second data header} );
+
 done_testing();

templates/qc_eval_metric_-v1.3-.yaml

@@ -28,6 +28,8 @@ wgs:
   collectmultiplemetrics:
     PCT_PF_READS_ALIGNED:
       lt: 0.95
+    PCT_PF_READS_IMPROPER_PAIRS:
+      gt: 0.05
     PCT_ADAPTER:
       gt: 0.0005
   markduplicates: