Merge 849412d into e223efb

Clinical-Genomics · Sep 8, 2022 · a417b70 · a417b70
2 parents e223efb + 849412d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,10 +9,13 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Run UPD and subsequently chromograph on unaffected children
 - Annotate SV variants with the caller that reported the variant
 - Produce files for CNV analysis in Gens
+- Updated SO terms for new version of VEP
+- ExACpLI -> pLI, see [vep issue 108](https://github.com/Ensembl/VEP_plugins/issues/108)
 
 ### Tools
 
 - Arriba: 2.1.0 -> 2.3.0
+- Chromograph 1.1.4 -> 1.1.5
 - DeepVariant: 1.1.0 -> 1.4.0
 - ExpansionHunter: 4.0.2 -> 5.0.0
 - GATK: 4.2.2.0 -> 4.2.6.1
@@ -24,14 +27,15 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Star Fusion: 1.10.1 -> 1.11.0
 - Stranger: 0.8.0 -> 0.8.1
 - Stringtie: 2.1.3b -> 2.2.1
-- svdb: 2.4.0 -> 2.6.4
-- Tiddit: 2.12.1 -> 3.1.0
+- Tiddit: 2.12.1 -> 3.3.1
 - Trimgalore: 0.6.4 -> 0.6.7
-- VEP: 104.3 -> 106.1
+- VEP: 104.3 -> 107.0
+- svdb: 2.4.0 -> 2.6.4
+- vcf2cytosure v0.5.1 -> v0.8
 
 ### Databases
 
-- clinvar: 211010 -> 220730
+- clinvar: 20211010 -> 20220829
 - dbnsfp: 4.1a -> 4.3a (grch38 only)
 - gnomad: r3.1.1 -> r3.1.2 (grch38 only)
 - giab: 3.3.2 -> 4.2.1

diff --git a/definitions/install_parameters.yaml b/definitions/install_parameters.yaml
@@ -206,7 +206,7 @@ vep_plugins:
   data_type: ARRAY
   default:
     - dbNSFP
-    - ExACpLI
+    - pLI
     - LoFtool
     - MaxEntScan
     - SpliceAI

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -250,6 +250,7 @@ recipe_core_number:
     sv_varianteffectpredictor: 0
     sv_vcfparser: 13
     telomerecat_ar: 12
+    tiddit: 12
     tiddit_coverage: 1
     upd_ar: 1
     varg_ar: 1
@@ -307,7 +308,7 @@ recipe_memory:
     sv_annotate: 7
     sv_reformat: 24
     sv_varianteffectpredictor: 9
-    tiddit: 8
+    tiddit: 5
     upd_ar: 3
     variant_annotation: 3
     varianteffectpredictor: 7
@@ -380,7 +381,7 @@ recipe_time:
     sv_varianteffectpredictor: 10
     sv_vcfparser: 2
     telomerecat_ar: 5
-    tiddit: 20
+    tiddit: 15
     tiddit_coverage: 5
     upd_ar: 1
     varg_ar: 1

diff --git a/documentation/Setup.md b/documentation/Setup.md
@@ -34,8 +34,8 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - Simple Linux Utility for Resource Management ([SLURM]) (version: 18.08.0)
 
 #### **Pipeline: Rare disease**
-- [Arriba] (version: 2.1.0)
-- [Bcftools] (version: 1.11)
+- [Arriba] (version: 2.3.0)
+- [Bcftools] (version: 1.15.1)
 - [BWA] (version: 0.7.17)
 - [BedTools] (version: 2.30.0)
 - [Blobfish] (version: 0.0.2 )
@@ -46,10 +46,10 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Chromograph] (version: 1.1.5)
 - [Cnvnator] (version: 0.4.1)
 - [Cyrius] (version: v1.1.1)
-- [Expansionhunter] (version 4.0.2)
+- [Expansionhunter] (version 5.0.0)
 - [FastQC] (version: 0.11.9)
-- [Deeptrio] (version: 1.2.0)
-- [Deepvariant] (version: 1.1.0)
+- [Deeptrio] (version: 1.4.0)
+- [Deepvariant] (version: 1.4.0)
 - [Delly] (version 0.8.7)
 - [GATK] (version: 3.8.1 and 4.2.2.0)
 - [GENMOD] (version: 3.7.3)
@@ -58,20 +58,20 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Htslib] (version: 1.13)
 - [Manta] (version: 1.6.0)
 - [Megafusion] (version: 66a3a80)
-- [MultiQC] (version: v1.11)
+- [MultiQC] (version: v1.12)
 - [Pdfmerger] (version: 1.0)
 - [Peddy] (version: 0.4.3)
-- [PicardTools] (version: 2.25.0)
+- [PicardTools] (version: 2.27.2)
 - [PLINK] (version: 1.90b3x35)
 - [Preseq] (version: 3.1.2)
 - [Rhocall] (version: 0.5.1)
 - [RSeQC] (version: 4.0.0)
 - [rtg-tools] (version: 3.12)
 - [Salmon] (version: 1.4.0)
 - [Sambamba] (version: 0.6.8)
-- [Samtools] (version: 1.11)
+- [Samtools] (version: 1.15.1)
 - [SMNCopyNumberCaller] (version: v1.1.1)
-- [STAR-Fusion] (version: 1.10.1)
+- [STAR-Fusion] (version: 1.11.0)
 - [STAR] (version: 2.7.8a)
 - [Stranger] (version: 0.8.0)
 - [StringTie] (version: 2.1.3b)
@@ -82,7 +82,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Varg] (version: 1.2.0)
 - [Vcf2cytosure] (version: 0.5.1)
 - [Vcfanno] (version: 0.3.2)
-- [VEP] (version: 104.3) with plugin "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI"
+- [VEP] (version: 107.0) with plugin "pLI", "MaxEntScan, LoFtool", "SpliceAI"
 
 The version number after the software name are tested for compatibility with MIP.
 

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -90,151 +90,159 @@ Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;
 Readonly our %SO_CONSEQUENCE_SEVERITY => (
     transcript_ablation => {
         rank                      => 1,
-        genetic_region_annotation => q{exonic}
-    },
-    splice_donor_variant => {
-        rank                      => 2,
-        genetic_region_annotation => q{splicing}
+        genetic_region_annotation => q{exonic},
     },
     splice_acceptor_variant => {
         rank                      => 2,
-        genetic_region_annotation => q{splicing}
+        genetic_region_annotation => q{splicing},
     },
-    stop_gained => {
+    splice_donor_variant => {
         rank                      => 3,
-        genetic_region_annotation => q{exonic}
+        genetic_region_annotation => q{splicing},
     },
-    frameshift_variant => {
+    stop_gained => {
         rank                      => 4,
-        genetic_region_annotation => q{exonic}
+        genetic_region_annotation => q{exonic},
     },
-    stop_lost => {
+    frameshift_variant => {
         rank                      => 5,
-        genetic_region_annotation => q{exonic}
+        genetic_region_annotation => q{exonic},
+    },
+    stop_lost => {
+        rank                      => 6,
+        genetic_region_annotation => q{exonic},
     },
     start_lost => {
-        rank                      => 5,
-        genetic_region_annotation => q{exonic}
+        rank                      => 7,
+        genetic_region_annotation => q{exonic},
     },
-    initiator_codon_variant => {
-        rank                      => 6,
-        genetic_region_annotation => q{exonic}
+    transcript_amplification => {
+        rank                      => 8,
+        genetic_region_annotation => q{exonic},
     },
     inframe_insertion => {
-        rank                      => 6,
-        genetic_region_annotation => q{exonic}
+        rank                      => 9,
+        genetic_region_annotation => q{exonic},
     },
     inframe_deletion => {
-        rank                      => 6,
-        genetic_region_annotation => q{exonic}
+        rank                      => 10,
+        genetic_region_annotation => q{exonic},
     },
     missense_variant => {
-        rank                      => 6,
-        genetic_region_annotation => q{exonic}
+        rank                      => 11,
+        genetic_region_annotation => q{exonic},
     },
     protein_altering_variant => {
-        rank                      => 6,
-        genetic_region_annotation => q{exonic}
-    },
-    transcript_amplification => {
-        rank                      => 7,
-        genetic_region_annotation => q{exonic}
+        rank                      => 12,
+        genetic_region_annotation => q{exonic},
     },
     splice_region_variant => {
-        rank                      => 8,
-        genetic_region_annotation => q{splicing}
+        rank                      => 13,
+        genetic_region_annotation => q{splicing},
+    },
+    splice_donor_5th_base_variant => {
+        rank                      => 14,
+        genetic_region_annotation => q{splicing},
+    },
+    splice_donor_region_variant => {
+        rank                      => 15,
+        genetic_region_annotation => q{splicing},
+    },
+    splice_polypyrimidine_tract_variant => {
+        rank                      => 16,
+        genetic_region_annotation => q{splicing},
     },
     incomplete_terminal_codon_variant => {
-        rank                      => 9,
-        genetic_region_annotation => q{exonic}
+        rank                      => 17,
+        genetic_region_annotation => q{exonic},
     },
-    synonymous_variant => {
-        rank                      => 10,
-        genetic_region_annotation => q{exonic}
+    start_retained_variant => {
+        rank                      => 18,
+        genetic_region_annotation => q{exonic},
     },
     stop_retained_variant => {
-        rank                      => 10,
-        genetic_region_annotation => q{exonic}
+        rank                      => 19,
+        genetic_region_annotation => q{exonic},
     },
-    start_retained_variant => {
-        rank                      => 10,
-        genetic_region_annotation => q{exonic}
+    synonymous_variant => {
+        rank                      => 20,
+        genetic_region_annotation => q{exonic},
     },
     coding_sequence_variant => {
-        rank                      => 11,
-        genetic_region_annotation => q{exonic}
+        rank                      => 21,
+        genetic_region_annotation => q{exonic},
     },
     mature_miRNA_variant => {
-        rank                      => 12,
-        genetic_region_annotation => q{ncRNA_exonic}
+        rank                      => 22,
+        genetic_region_annotation => q{ncRNA_exonic},
     },
     q{5_prime_UTR_variant} => {
-        rank                      => 13,
-        genetic_region_annotation => q{5UTR}
+        rank                      => 23,
+        genetic_region_annotation => q{5UTR},
     },
     q{3_prime_UTR_variant} => {
-        rank                      => 14,
-        genetic_region_annotation => q{3UTR}
+        rank                      => 24,
+        genetic_region_annotation => q{3UTR},
     },
     non_coding_transcript_exon_variant => {
-        rank                      => 15,
-        genetic_region_annotation => q{ncRNA_exonic}
-    },
-    non_coding_transcript_variant => {
-        rank                      => 15,
-        genetic_region_annotation => q{ncRNA}
+        rank                      => 25,
+        genetic_region_annotation => q{ncRNA_exonic},
     },
     intron_variant => {
-        rank                      => 16,
-        genetic_region_annotation => q{intronic}
+        rank                      => 26,
+        genetic_region_annotation => q{intronic},
     },
     NMD_transcript_variant => {
-        rank                      => 17,
-        genetic_region_annotation => q{ncRNA}
+        rank                      => 27,
+        genetic_region_annotation => q{ncRNA},
+    },
+    non_coding_transcript_variant => {
+        rank                      => 28,
+        genetic_region_annotation => q{ncRNA},
     },
     upstream_gene_variant => {
-        rank                      => 18,
-        genetic_region_annotation => q{upstream}
+        rank                      => 29,
+        genetic_region_annotation => q{upstream},
     },
     downstream_gene_variant => {
-        rank                      => 19,
-        genetic_region_annotation => q{downstream}
+        rank                      => 30,
+        genetic_region_annotation => q{downstream},
     },
     TFBS_ablation => {
-        rank                      => 20,
-        genetic_region_annotation => q{TFBS}
+        rank                      => 31,
+        genetic_region_annotation => q{TFBS},
     },
     TFBS_amplification => {
-        rank                      => 21,
-        genetic_region_annotation => q{TFBS}
+        rank                      => 32,
+        genetic_region_annotation => q{TFBS},
     },
     TF_binding_site_variant => {
-        rank                      => 22,
-        genetic_region_annotation => q{TFBS}
-    },
-    regulatory_region_variant => {
-        rank                      => 22,
-        genetic_region_annotation => q{regulatory_region}
+        rank                      => 33,
+        genetic_region_annotation => q{TFBS},
     },
     regulatory_region_ablation => {
-        rank                      => 23,
-        genetic_region_annotation => q{regulatory_region}
+        rank                      => 34,
+        genetic_region_annotation => q{regulatory_region},
     },
     regulatory_region_amplification => {
-        rank                      => 24,
-        genetic_region_annotation => q{regulatory_region}
+        rank                      => 35,
+        genetic_region_annotation => q{regulatory_region},
     },
     feature_elongation => {
-        rank                      => 25,
-        genetic_region_annotation => q{genomic_feature}
+        rank                      => 36,
+        genetic_region_annotation => q{genomic_feature},
+    },
+    regulatory_region_variant => {
+        rank                      => 37,
+        genetic_region_annotation => q{regulatory_region},
     },
     feature_truncation => {
-        rank                      => 26,
-        genetic_region_annotation => q{genomic_feature}
+        rank                      => 38,
+        genetic_region_annotation => q{genomic_feature},
     },
     intergenic_variant => {
-        rank                      => 27,
-        genetic_region_annotation => q{intergenic}
+        rank                      => 39,
+        genetic_region_annotation => q{intergenic},
     },
 );