From 7b73620ad002207c2d9a3dc6418f64105c73a366 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Wed, 25 Aug 2021 13:37:52 +0200
Subject: [PATCH] turning off haplotypecaller

---
 CHANGELOG.md                            |  2 ++
 definitions/rd_dna_parameters.yaml      | 13 ++++++++-----
 lib/MIP/Cli/Mip/Analyse/Rd_dna.pm       |  1 +
 templates/grch38_mip_rd_dna_config.yaml |  4 ----
 templates/mip_rd_dna_config.yaml        |  4 ----
 5 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b773341e6..03cbb905f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [Develop]
 
 - HmtNote: annotate mitochondrial variants in VCF file
+- Mitochondrial deletion analysis
+- GATK Haplotypecaller has been turned off in favour of Deepvariant
 
 ### Tools
 
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
index d92fc3ff9..9ebf11f6e 100755
--- a/definitions/rd_dna_parameters.yaml
+++ b/definitions/rd_dna_parameters.yaml
@@ -523,7 +523,7 @@ gatk_baserecalibration:
   associated_recipe:
     - mip
   data_type: SCALAR
-  default: 1
+  default: 0
   file_tag: _brecal
   outfile_suffix: ".bam"
   program_executables:
@@ -1192,7 +1192,7 @@ gatk_haplotypecaller:
   associated_recipe:
     - mip
   data_type: SCALAR
-  default: 1
+  default: 0
   file_tag: _haptc
   outfile_suffix: ".vcf"
   program_executables:
@@ -1263,7 +1263,7 @@ gatk_genotypegvcfs:
   associated_recipe:
     - mip
   data_type: SCALAR
-  default: 1
+  default: 0
   file_tag: _gent
   outfile_suffix: ".vcf"
   program_executables:
@@ -1288,7 +1288,7 @@ gatk_gathervcfs:
   associated_recipe:
     - mip
   data_type: SCALAR
-  default: 1
+  default: 0
   file_tag: ""
   outfile_suffix: ".vcf"
   program_executables:
@@ -1306,7 +1306,7 @@ gatk_variantrecalibration:
   associated_recipe:
     - mip
   data_type: SCALAR
-  default: 1
+  default: 0
   file_tag: _vrecal
   program_executables:
     - bcftools
@@ -1459,12 +1459,15 @@ gatk_combinevariants_prioritize_caller:
   associated_recipe:
     - gatk_combinevariantcallsets
   data_type: SCALAR
+  default: deepvariant
   mandatory: no
   type: recipe_argument
 gatk_combinevariants_callers_to_combine:
   associated_recipe:
     - gatk_combinevariantcallsets
   data_type: ARRAY
+  default:
+    - glnexus_merge
   mandatory: no
   type: recipe_argument
 prepareforvariantannotationblock:
diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
index 964e7fe8a..97b31e119 100644
--- a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
+++ b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
@@ -1397,6 +1397,7 @@ q{Number of hom-ref genotypes to infer at sites not present in a panel. Connecte
         q{gatk_combinevariants_callers_to_combine} => (
             cmd_flag      => q{gatk_combinevar_use_callers},
             documentation => q{Combine vcf output from these recipes},
+            cmd_tags      => [q{Defaults: glnexus_merge}],
             is            => q{rw},
             isa           => ArrayRef [ enum( [qw{ gatk_variantrecalibration glnexus_merge }] ), ],
         )
diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml
index 71f39299b..f5134c3ed 100755
--- a/templates/grch38_mip_rd_dna_config.yaml
+++ b/templates/grch38_mip_rd_dna_config.yaml
@@ -66,10 +66,6 @@ vcfanno_config: grch38_vcfanno_config_-v0.2-.toml
 ### Analysis
 ## Programs
 ## Parameters
-gatk_combinevariants_prioritize_caller: deepvariant,haplotypecaller
-gatk_combinevariants_callers_to_combine:
-  - gatk_variantrecalibration
-  - glnexus_merge
 gatk_path: /opt/conda/opt/gatk-3.8
 qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
 picardtools_path: /usr/picard/
diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml
index 5745445b7..96a0b9f79 100755
--- a/templates/mip_rd_dna_config.yaml
+++ b/templates/mip_rd_dna_config.yaml
@@ -47,10 +47,6 @@ fqf_annotations:
   - GNOMADAF
   - GNOMADAF_popmax
   - SWEGENAF
-gatk_combinevariants_prioritize_caller: deepvariant,haplotypecaller
-gatk_combinevariants_callers_to_combine:
-  - gatk_variantrecalibration
-  - glnexus_merge
 gatk_path: /usr
 picardtools_path: /usr/picard
 qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml