Merge 6312906 into 0f97d7e

Clinical-Genomics · Sep 23, 2021 · 893b13b · 893b13b
2 parents 0f97d7e + 6312906
commit 893b13b
Show file tree

Hide file tree

Showing 39 changed files with 76 additions and 69 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,7 @@ vep release_103.1 -> release_104.3
 
 - gnomad: r3.0 -> r3.1.1
 - [NEW] gnomad mt: r3.1
+- clinvar: 20210415 -> 20210919
 
 ## [10.2.1]
 

diff --git a/t/check_vep_api_cache_versions.t b/t/check_vep_api_cache_versions.t
@@ -54,13 +54,13 @@ my $test_dir = File::Temp->newdir();
 test_log( {} );
 
 ## Given matching vep API and cache version
-my $vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data-103 cache } );
+my $vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data-104 cache } );
 
 my %process_return = (
     buffers_ref   => [],
     error_message => undef,
     stderrs_ref   => [],
-    stdouts_ref   => [qw{ 103 }],
+    stdouts_ref   => [qw{ 104 }],
     success       => 1,
 );
 test_constants(
@@ -70,7 +70,7 @@ test_constants(
 );
 my $base_command = q{vep};
 my $container_base_command =
-  q{singularity exec docker//docker.io/ensemblorg/ensembl-vep:release_103.1 vep};
+  q{singularity exec docker//docker.io/ensemblorg/ensembl-vep:release_104.3 vep};
 my %container_cmd = ( $base_command => $container_base_command, );
 set_container_cmd( { container_cmd_href => \%container_cmd, } );
 
@@ -85,7 +85,7 @@ my $match = check_vep_api_cache_versions(
 ok( $match, q{Return on matching versions} );
 
 ## Given non matching API and cache
-$vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data-103 cache2 } );
+$vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data-104 cache2 } );
 
 ## When comparing API and cache version
 trap {

diff --git a/...l-tools-103/cache/cache/Plugins/Hello.txt → ...ensembl-tools-104/cache/Plugins/Hello.txt b/...l-tools-103/cache/cache/Plugins/Hello.txt → ...ensembl-tools-104/cache/Plugins/Hello.txt
diff --git a/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt b/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt
diff --git a/...103/cache/cache/Plugins/human_ancestor.fa → ...tools-104/cache/Plugins/human_ancestor.fa b/...103/cache/cache/Plugins/human_ancestor.fa → ...tools-104/cache/Plugins/human_ancestor.fa
diff --git a/...l-tools-data-103/cache/Plugins/ExACpLI.pm → ...l-tools-data-104/cache/Plugins/ExACpLI.pm b/...l-tools-data-103/cache/Plugins/ExACpLI.pm → ...l-tools-data-104/cache/Plugins/ExACpLI.pm
diff --git a/...bl-tools-data-103/cache/Plugins/Hello.txt → ...bl-tools-data-104/cache/Plugins/Hello.txt b/...bl-tools-data-103/cache/Plugins/Hello.txt → ...bl-tools-data-104/cache/Plugins/Hello.txt
diff --git a/...l-tools-data-103/cache/Plugins/LoFtool.pm → ...l-tools-data-104/cache/Plugins/LoFtool.pm b/...l-tools-data-103/cache/Plugins/LoFtool.pm → ...l-tools-data-104/cache/Plugins/LoFtool.pm
diff --git a/...data-103/cache/Plugins/LoFtool_scores.txt → ...data-104/cache/Plugins/LoFtool_scores.txt b/...data-103/cache/Plugins/LoFtool_scores.txt → ...data-104/cache/Plugins/LoFtool_scores.txt
diff --git a/...ools-data-103/cache/Plugins/MaxEntScan.pm → ...ools-data-104/cache/Plugins/MaxEntScan.pm b/...ools-data-103/cache/Plugins/MaxEntScan.pm → ...ools-data-104/cache/Plugins/MaxEntScan.pm
diff --git a/...-tools-data-103/cache/Plugins/SpliceAI.pm → ...-tools-data-104/cache/Plugins/SpliceAI.pm b/...-tools-data-103/cache/Plugins/SpliceAI.pm → ...-tools-data-104/cache/Plugins/SpliceAI.pm
diff --git a/...bl-tools-data-103/cache/Plugins/dbNSFP.pm → ...bl-tools-data-104/cache/Plugins/dbNSFP.pm b/...bl-tools-data-103/cache/Plugins/dbNSFP.pm → ...bl-tools-data-104/cache/Plugins/dbNSFP.pm
diff --git a/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt b/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt
diff --git a/...-data-103/cache/Plugins/human_ancestor.fa → ...-data-104/cache/Plugins/human_ancestor.fa b/...-data-103/cache/Plugins/human_ancestor.fa → ...-data-104/cache/Plugins/human_ancestor.fa
diff --git a/...3/cache/homo_sapiens/103_GRCh37/Hello.txt → ...4/cache/homo_sapiens/104_GRCh37/Hello.txt b/...3/cache/homo_sapiens/103_GRCh37/Hello.txt → ...4/cache/homo_sapiens/104_GRCh37/Hello.txt
diff --git a/...03/cache/homo_sapiens/95_GRCh37/Hello.txt → ...04/cache/homo_sapiens/95_GRCh37/Hello.txt b/...03/cache/homo_sapiens/95_GRCh37/Hello.txt → ...04/cache/homo_sapiens/95_GRCh37/Hello.txt
diff --git a/...03/cache/homo_sapiens/97_GRCh37/Hello.txt → ...04/cache/homo_sapiens/97_GRCh37/Hello.txt b/...03/cache/homo_sapiens/97_GRCh37/Hello.txt → ...04/cache/homo_sapiens/97_GRCh37/Hello.txt
diff --git a/...03/cache/homo_sapiens/99_GRCh37/Hello.txt → ...04/cache/homo_sapiens/99_GRCh37/Hello.txt b/...03/cache/homo_sapiens/99_GRCh37/Hello.txt → ...04/cache/homo_sapiens/99_GRCh37/Hello.txt
diff --git a/.../homo_sapiens_merged/103_GRCh37/Hello.txt → .../homo_sapiens_merged/104_GRCh37/Hello.txt b/.../homo_sapiens_merged/103_GRCh37/Hello.txt → .../homo_sapiens_merged/104_GRCh37/Hello.txt
diff --git a/...e/homo_sapiens_merged/95_GRCh37/Hello.txt → ...e/homo_sapiens_merged/95_GRCh37/Hello.txt b/...e/homo_sapiens_merged/95_GRCh37/Hello.txt → ...e/homo_sapiens_merged/95_GRCh37/Hello.txt
diff --git a/...e/homo_sapiens_merged/97_GRCh37/Hello.txt → ...e/homo_sapiens_merged/97_GRCh37/Hello.txt b/...e/homo_sapiens_merged/97_GRCh37/Hello.txt → ...e/homo_sapiens_merged/97_GRCh37/Hello.txt
diff --git a/...3/cache2/homo_sapiens/95_GRCh37/Hello.txt → ...4/cache2/homo_sapiens/95_GRCh37/Hello.txt b/...3/cache2/homo_sapiens/95_GRCh37/Hello.txt → ...4/cache2/homo_sapiens/95_GRCh37/Hello.txt
diff --git a/...2/homo_sapiens_merged/95_GRCh37/Hello.txt → ...2/homo_sapiens_merged/95_GRCh37/Hello.txt b/...2/homo_sapiens_merged/95_GRCh37/Hello.txt → ...2/homo_sapiens_merged/95_GRCh37/Hello.txt
diff --git a/...ch37_clinvar_reformated_-20210415-.vcf.gz → ...ch37_clinvar_reformated_-20210919-.vcf.gz b/...ch37_clinvar_reformated_-20210415-.vcf.gz → ...ch37_clinvar_reformated_-20210919-.vcf.gz
diff --git a/..._clinvar_reformated_-20210415-.vcf.gz.tbi → ..._clinvar_reformated_-20210919-.vcf.gz.tbi b/..._clinvar_reformated_-20210415-.vcf.gz.tbi → ..._clinvar_reformated_-20210919-.vcf.gz.tbi
diff --git a/..._loqusdb_sv_variants_export-20210416-.vcf → ..._loqusdb_sv_variants_export-20210921-.vcf b/..._loqusdb_sv_variants_export-20210416-.vcf → ..._loqusdb_sv_variants_export-20210921-.vcf
diff --git a/...ch38_clinvar_reformated_-20210415-.vcf.gz → ...ch38_clinvar_reformated_-20210919-.vcf.gz b/...ch38_clinvar_reformated_-20210415-.vcf.gz → ...ch38_clinvar_reformated_-20210919-.vcf.gz
diff --git a/..._clinvar_reformated_-20210415-.vcf.gz.tbi → ..._clinvar_reformated_-20210919-.vcf.gz.tbi b/..._clinvar_reformated_-20210415-.vcf.gz.tbi → ..._clinvar_reformated_-20210919-.vcf.gz.tbi
diff --git a/t/data/references/grch38_gencode_annotation_-v38-.gtf b/t/data/references/grch38_gencode_annotation_-v38-.gtf
diff --git a/t/data/references/grch38_gencode_transcripts_-v38-.fa b/t/data/references/grch38_gencode_transcripts_-v38-.fa
diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml
@@ -94,10 +94,10 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch38_clinvar_reformated_-20210415-.vcf.gz
+    path: cluster_constant_path!/references/grch38_clinvar_reformated_-20210919-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-103/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
 vep_plugin:
   dbNSFP:
     exist_check:
@@ -119,15 +119,15 @@ vep_plugin:
   LoFtool:
     exists_check:
       - type: file
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exist_check:
       - type: directory
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
       - SWA
       - NCSS
   SpliceAI:

diff --git a/templates/grch38_mip_rd_rna_config.yaml b/templates/grch38_mip_rd_rna_config.yaml
@@ -41,4 +41,4 @@ fusion_cytoband_path: /arriba_v2.1.0/database/cytobands_hg38_GRCh38_v2.1.0.tsv
 fusion_protein_domain_path: /arriba_v2.1.0/database/protein_domains_hg38_GRCh38_v2.1.0.gff3
 picardtools_path: /usr/picard
 qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
-vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-103/cache/
+vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-104/cache/
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -26,8 +26,8 @@ reference:
   chromograph_cytoband:
     - v1.0
   clinvar:
-    - 20200905
     - 20210415
+    - 20210919
   dbnsfp:
     - 3.5a
     - 4.0b2a
@@ -122,8 +122,8 @@ reference:
     - 1.0
   vcfanno_config:
     - v0.2
-    - v1.15
     - v1.16
+    - v1.17
   vcfanno_functions:
     - v1.0
 reference_feature:
@@ -314,15 +314,6 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
   clinvar:
     grch37:
-      20200905:
-        file: clinvar_20200905.vcf.gz
-        file_check: clinvar_20200905.vcf.gz.md5
-        file_index: clinvar_20200905.vcf.gz.tbi
-        outfile: grch37_clinvar_-20200905-.vcf.gz
-        outfile_check: grch37_clinvar_-20200905-.vcf.gz.md5
-        outfile_index: grch37_clinvar_-20200905-.vcf.gz.tbi
-        outfile_check_method: md5sum
-        url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2020/
       20210415:
         file: clinvar_20210415.vcf.gz
         file_check: clinvar_20210415.vcf.gz.md5
@@ -332,6 +323,15 @@ reference_feature:
         outfile_index: grch37_clinvar_-20210415-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
+      20210919:
+        file: clinvar_20210919.vcf.gz
+        file_check: clinvar_20210919.vcf.gz.md5
+        file_index: clinvar_20210919.vcf.gz.tbi
+        outfile: grch37_clinvar_-20210919-.vcf.gz
+        outfile_check: grch37_clinvar_-20210919-.vcf.gz.md5
+        outfile_index: grch37_clinvar_-20210919-.vcf.gz.tbi
+        outfile_check_method: md5sum
+        url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly
     grch38:
       20200905:
         file: clinvar_20200905.vcf.gz
@@ -902,20 +902,20 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
   vcfanno_config:
     grch37:
-      v1.15:
-        file: grch37_vcfanno_config_-v1.15-.toml
-        file_check: grch37_vcfanno_config_-v1.15-.toml.md5
-        outfile: grch37_vcfanno_config_-v1.15-.toml
-        outfile_check: grch37_vcfanno_config_-v1.15-.toml.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
       v1.16:
         file: grch37_vcfanno_config_-v1.16-.toml
         file_check: grch37_vcfanno_config_-v1.16-.toml.md5
         outfile: grch37_vcfanno_config_-v1.16-.toml
         outfile_check: grch37_vcfanno_config_-v1.16-.toml.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
+      v1.17:
+        file: grch37_vcfanno_config_-v1.17-.toml
+        file_check: grch37_vcfanno_config_-v1.17-.toml.md5
+        outfile: grch37_vcfanno_config_-v1.17-.toml
+        outfile_check: grch37_vcfanno_config_-v1.17-.toml.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
     grch38:
       v0.2:
         file: grch38_vcfanno_config_-v0.2-.toml

diff --git a/templates/mip_download_rd_rna_config_-1.0-.yaml b/templates/mip_download_rd_rna_config_-1.0-.yaml
@@ -16,10 +16,11 @@ reference:
     - gold_standard_dbsnp
     - 146
   gencode_annotation:
-    - v34
     - v37
+    - v38
   gencode_transcript:
     - v37
+    - v38
   human_reference:
     - decoy_5
     - assembly38
@@ -42,16 +43,16 @@ reference_feature:
         outfile_decompress: gzip
         url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/GRCh37_mapping/
     grch38:
-      v34:
-        file: gencode.v34.annotation.gtf.gz
-        outfile: grch38_gencode_annotation_-v34-.gtf.gz
-        outfile_decompress: gzip
-        url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/
       v37:
         file: gencode.v37.primary_assembly.annotation.gtf.gz
         outfile: grch38_gencode_annotation_-v37-.gtf.gz
         outfile_decompress: gzip
         url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/
+      v38:
+        file: gencode.v38.primary_assembly.annotation.gtf.gz
+        outfile: grch38_gencode_annotation_-v38-.gtf.gz
+        outfile_decompress: gzip
+        url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/
   gencode_transcript:
     grch37:
       v37:
@@ -65,6 +66,11 @@ reference_feature:
         outfile: grch38_gencode_transcripts_-v37-.fa.gz
         outfile_decompress: gzip
         url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/
+      v38:
+        file: gencode.v38.transcripts.fa.gz
+        outfile: grch38_gencode_transcripts_-v38-.fa.gz
+        outfile_decompress: gzip
+        url_prefix: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/
   ctat_resource_lib:
     grch37:
       gencode_v19_ctat_lib_mar012021:

diff --git a/templates/mip_dragen_rd_dna_config.yaml b/templates/mip_dragen_rd_dna_config.yaml
@@ -68,10 +68,10 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210415-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210919-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-103/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
 vep_plugin:
   dbNSFP:
     exist_check:
@@ -93,15 +93,15 @@ vep_plugin:
   LoFtool:
     exist_check:
       - type: file
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exist_check:
       - type: directory
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
       - SWA
       - NCSS
   SpliceAI:

diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml
@@ -31,15 +31,15 @@ sv_rank_model_file: svrank_model_-v1.8-.ini
 sv_svdb_query_db_files:
   # FORMAT: filename|OUT_FREQUENCY_INFO_KEY|OUT_ALLELE_COUNT_INFO_KEY|IN_FREQUENCY_INFO_KEY|IN_ALLELE_COUNT_INFO_KEY|USE_IN_FREQUENCY_FILTER
   grch37_gnomad_reformated_-r2.1.1_sv-.vcf.gz: gnomad_sv|AF|AC|AF|AC|1
-  grch37_loqusdb_sv_variants_export-20210416-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs
+  grch37_loqusdb_sv_variants_export-20210921-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs|1
   grch37_mip_sv_svdb_export_-2018-10-09-.vcf: clinical_genomics_mip|AF|OCC|FRQ|OCC|1
   grch37_svdb_query_decipher_-v1.0.0-.vcf: decipher|AF|OCC|FRQ|OCC
   grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf: clingen_cgh_benign
   grch37_svdb_query_clingen_cgh_pathogenic_-v1.0.0-.vcf: clingen_cgh_pathogenic
   grch37_svdb_query_clingen_ngi_-v1.0.0-.vcf: clingen_ngi|AF|OCC|FRQ|OCC|1
   grch37_swegen_concat_sort_-20170830-.vcf: swegen|AF|OCC|FRQ|OCC|1
 vcf2cytosure_blacklist: grch37_cytosure_blacklist_-1.0-.bed
-vcfanno_config: grch37_vcfanno_config_-v1.16-.toml
+vcfanno_config: grch37_vcfanno_config_-v1.17-.toml
 ### Analysis
 ### Programs
 ## Parameters
@@ -75,10 +75,10 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210415-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210919-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-103/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
 vep_plugin:
   dbNSFP:
     exist_check:
@@ -100,15 +100,15 @@ vep_plugin:
   LoFtool:
     exist_check:
       - type: file
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exist_check:
       - type: directory
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
       - SWA
       - NCSS
   SpliceAI:

diff --git a/templates/mip_rd_dna_panel_config.yaml b/templates/mip_rd_dna_panel_config.yaml
@@ -49,10 +49,10 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210415-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210919-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-103/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
 vep_plugin:
   dbNSFP:
     exist_check:
@@ -74,15 +74,15 @@ vep_plugin:
   LoFtool:
     exist_check:
       - type: file
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exist_check:
       - type: directory
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
       - SWA
       - NCSS
   SpliceAI:

diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml
@@ -28,15 +28,15 @@ sv_rank_model_file: svrank_model_-v1.8-.ini
 # FORMAT: filename|OUT_FREQUENCY_INFO_KEY|OUT_ALLELE_COUNT_INFO_KEY|IN_FREQUENCY_INFO_KEY|IN_ALLELE_COUNT_INFO_KEY|USE_IN_FREQUENCY_FILTER
 sv_svdb_query_db_files:
   grch37_gnomad_reformated_-r2.1.1_sv-.vcf.gz: gnomad_sv|AF|AC|AF|AC|1
-  grch37_loqusdb_sv_variants_export-20210416-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs
+  grch37_loqusdb_sv_variants_export-20210921-.vcf: clinical_genomics_loqus|Frq|Obs|Frq|Obs
   grch37_mip_sv_svdb_export_-2018-10-09-.vcf: clinical_genomics_mip|AF|OCC|FRQ|OCC|1
   grch37_svdb_query_decipher_-v1.0.0-.vcf: decipher|AF|OCC|FRQ|OCC
   grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf: clingen_cgh_benign
   grch37_svdb_query_clingen_cgh_pathogenic_-v1.0.0-.vcf: clingen_cgh_pathogenic
   grch37_svdb_query_clingen_ngi_-v1.0.0-.vcf: clingen_ngi|AF|OCC|FRQ|OCC|1
   grch37_swegen_concat_sort_-20170830-.vcf: swegen|AF|OCC|FRQ|OCC|1
 sv_vcfanno_config: grch37_sv_vcfanno_config_-v1.4-.toml
-vcfanno_config: grch37_vcfanno_config_-v1.16-.toml
+vcfanno_config: grch37_vcfanno_config_-v1.17-.toml
 ### Analysis
 ## Programs
 ## Parameters
@@ -70,10 +70,10 @@ vep_custom_annotation:
     force_report_coordinates: 0
     key: CLINVAR
     file_type: vcf
-    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210415-.vcf.gz
+    path: cluster_constant_path!/references/grch37_clinvar_reformated_-20210919-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-103/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins
 vep_plugin:
   dbNSFP:
     exist_check:
@@ -95,15 +95,15 @@ vep_plugin:
   LoFtool:
     exist_check:
       - type: file
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/LoFtool_scores.txt
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exist_check:
       - type: directory
-        path: cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+        path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
     parameters:
-      - cluster_constant_path!/references/ensembl-tools-data-103/cache/Plugins/fordownload
+      - cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins/fordownload
       - SWA
       - NCSS
   SpliceAI:

diff --git a/templates/mip_rd_rna_config.yaml b/templates/mip_rd_rna_config.yaml
@@ -33,4 +33,4 @@ fusion_cytoband_path: /arriba_v2.1.0/database/cytobands_hg19_hs37d5_GRCh37_v2.1.
 fusion_protein_domain_path: /arriba_v2.1.0/database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3
 picardtools_path: /usr/picard
 qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
-vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-103/cache/
+vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-104/cache/