From 16cd580a0e364e0c19e0d2fd195c7dde705db2a9 Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Wed, 29 Apr 2026 13:30:48 +0200 Subject: [PATCH 1/2] Removed too much in a previous PR --- .../illumina/genmod/svrank_model_-v1.8-.ini | 418 +++++++++++++++++- 1 file changed, 417 insertions(+), 1 deletion(-) diff --git a/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini b/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini index 923e0c993..2fdc21259 100644 --- a/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini +++ b/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini @@ -3,9 +3,158 @@ name = svrank_model [Categories] + [[allele_frequency]] + category_aggregation = min + + [[clinical_significance]] + category_aggregation = sum + + [[consequence]] + category_aggregation = max + + [[gene_intolerance_prediction]] + category_aggregation = sum + + [[inheritance_models]] + category_aggregation = min + + [[variant_call_quality_filter]] + category_aggregate = sum + [[variant_length]] category_aggregation = min + [[variant_type]] + category_aggregation = min + +[gnomad_sv] + category = allele_frequency + data_type = float + description = Gnomad sv genomes frequency + field = INFO + info_key = gnomad_svAF + record_rule = max + separators = ',', + + [[not_reported]] + score = 6 + + [[common]] + score = -12 + lower = 0.02 + upper = 1.1 + + [[intermediate]] + score = 1 + lower = 0.005 + upper = 0.02 + + [[rare]] + score = 2 + lower = 0.0005 + upper = 0.005 + + [[very_rare]] + score = 4 + lower = 0 + upper = 0.0005 + +[swegen] + category = allele_frequency + data_type = float + description = Swegen genomes frequency + field = INFO + info_key = swegenAF + record_rule = max + separators = ',', + + [[not_reported]] + score = 6 + + [[common]] + score = -12 + lower = 0.02 + upper = 1.1 + + [[intermediate]] + score = 1 + lower = 0.005 + upper = 0.02 + + [[rare]] + score = 2 + lower = 0.0005 + upper = 0.005 + + [[very_rare]] + score = 4 + lower = 0 + upper = 0.0005 + +[svdb_merge_mip] + category = allele_frequency + data_type = float + description = Clinical genomics genomes frequency + field = INFO + info_key = clinical_genomics_mipAF + record_rule = max + separators = ',', + + [[not_reported]] + score = 6 + + [[common]] + score = -12 + lower = 0.02 + upper = 1.1 + + [[intermediate]] + score = 1 + lower = 0.005 + upper = 0.02 + + [[rare]] + score = 2 + lower = 0.0005 + upper = 0.005 + + [[very_rare]] + score = 4 + lower = 0 + upper = 0.0005 + +[clingen_ngi] + category = allele_frequency + data_type = float + description = clingen ngi genomes frequency + field = INFO + info_key = clingen_ngiAF + record_rule = max + separators = ',', + + [[not_reported]] + score = 6 + + [[common]] + score = -12 + lower = 0.05 + upper = 2.75 + + [[intermediate]] + score = 1 + lower = 0.0125 + upper = 0.05 + + [[rare]] + score = 2 + lower = 0.00125 + upper = 0.0125 + + [[very_rare]] + score = 4 + lower = 0 + upper = 0.00125 + [sv_len] category = variant_length data_type = integer @@ -36,4 +185,271 @@ [[medium_neg]] score = 3 lower = -1000000 - upper = -50001 \ No newline at end of file + upper = -50001 + +[gene_intolerance_score] + category = gene_intolerance_prediction + data_type = float + description = Gnomad gene intolerance prediction + field = INFO + info_key = most_severe_pli + record_rule = max + separators = None + + [[not_reported]] + score = 0 + + [[low_intolerance]] + score = 0 + lower = 0 + upper = 0.90 + + [[medium_intolerance]] + score = 2 + lower = 0.90 + upper = 0.99 + + [[high_intolerance]] + score = 4 + lower = 0.99 + upper = 1.1 + +[clingen_cgh_benign] + category = clinical_significance + data_type = integer + description = Clinical significance + field = INFO + info_key = clingen_cgh_benign + record_rule = max + separators = None + + [[not_reported]] + score = 0 + + [[benign]] + score = -12 + value = 1 + +[clingen_cgh_pathogenic] + category = clinical_significance + data_type = integer + description = Clinical significance + field = INFO + info_key = clingen_cgh_pathogenic + record_rule = max + separators = None + + [[not_reported]] + score = 0 + + [[pathogenic]] + score = 12 + value = 1 + +[most_severe_consequence] + category = consequence + data_type = string + description = The most severe consequence for this variant + field = INFO + info_key = most_severe_consequence + record_rule = max + separators = ',', ':', '|', + + [[transcript_ablation]] + score = 10 + priority = 6 + string = 'transcript_ablation' + + [[initiator_codon_variant]] + score = 9 + priority = 5 + string = 'initiator_codon_variant' + + [[frameshift_variant]] + score = 8 + priority = 5 + string = 'frameshift_variant' + + [[stop_gained]] + score = 8 + priority = 5 + string = 'stop_gained' + + [[start_lost]] + score = 8 + priority = 5 + string = 'start_lost' + + [[stop_lost]] + score = 8 + priority = 5 + string = 'stop_lost' + + [[splice_acceptor_variant]] + score = 8 + priority = 5 + string = 'splice_acceptor_variant' + + [[splice_donor_variant]] + score = 8 + priority = 5 + string = 'splice_donor_variant' + + [[coding_sequence_variant]] + score = 7 + priority = 4 + string = 'coding_sequence_variant' + + [[inframe_deletion]] + score = 5 + priority = 4 + string = 'inframe_deletion' + + [[transcript_amplification]] + score = 5 + priority = 4 + string = 'transcript_amplification' + + [[splice_region_variant]] + score = 5 + priority = 4 + string = 'splice_region_variant' + + [[missense_variant]] + score = 5 + priority = 4 + string = 'missense_variant' + + [[protein_altering_variant]] + score = 5 + priority = 4 + string = 'protein_altering_variant' + + [[inframe_insertion]] + score = 5 + priority = 4 + string = 'inframe_insertion' + + [[incomplete_terminal_codon_variant]] + score = 5 + priority = 4 + string = 'incomplete_terminal_codon_variant' + + [[non_coding_transcript_exon_variant]] + score = 3 + priority = 2 + string = 'non_coding_transcript_exon_variant' + + [[synonymous_variant]] + score = 2 + priority = 2 + string = 'synonymous_variant' + + [[mature_mirna_variant]] + score = 1 + priority = 2 + string = 'mature_mirna_variant' + + [[non_coding_transcript_variant]] + score = 1 + priority = 2 + string = 'non_coding_transcript_variant' + + [[regulatory_region_variant]] + score = 1 + priority = 2 + string = 'regulatory_region_variant' + + [[upstream_gene_variant]] + score = 1 + priority = 2 + string = 'upstream_gene_variant' + + [[regulatory_region_amplification]] + score = 1 + priority = 2 + string = 'regulatory_region_amplification' + + [[tfbs_amplification]] + score = 1 + priority = 2 + string = 'tfbs_amplification' + + [[5_prime_utr_variant]] + score = 1 + priority = 2 + string = '5_prime_utr_variant' + + [[intron_variant]] + score = 1 + priority = 2 + string = 'intron_variant' + + [[3_prime_utr_variant]] + score = 1 + priority = 2 + string = '3_prime_utr_variant' + + [[feature_truncation]] + score = 1 + priority = 2 + string = 'feature_truncation' + + [[TF_binding_site_variant]] + score = 1 + priority = 2 + string = 'TF_binding_site_variant' + + [[stop_retained_variant]] + score = 1 + priority = 2 + string = 'stop_retained_variant' + + [[feature_elongation]] + score = 1 + priority = 2 + string = 'feature_elongation' + + [[regulatory_region_ablation]] + score = 1 + priority = 2 + string = 'regulatory_region_ablation' + + [[tfbs_ablation]] + score = 1 + priority = 2 + string = 'tfbs_ablation' + + [[downstream_gene_variant]] + score = 1 + priority = 2 + string = 'downstream_gene_variant' + + [[NMD_transcript_variant]] + score = 1 + priority = 2 + string = 'NMD_transcript_variant' + + [[intergenic_variant]] + score = 0 + priority = 0 + string = 'intergenic_variant' + + [[not_reported]] + score = 0 + +[filter] + category = variant_call_quality_filter + data_type = string + description = The filters for the variant + field = FILTER + record_rule = min + separators = ';', + + [[not_reported]] + score = 0 + + [[pass]] + score = 3 + priority = 1 + string = 'PASS' \ No newline at end of file From 41859ddbf73fc2611616a9091dbb9f44b352e324 Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Mon, 4 May 2026 13:39:56 +0200 Subject: [PATCH 2/2] Revert #2022 completely --- .../illumina/genmod/svrank_model_-v1.8-.ini | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) diff --git a/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini b/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini index 2fdc21259..8cc0175fc 100644 --- a/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini +++ b/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini @@ -246,6 +246,90 @@ score = 12 value = 1 +[genetic_models] + data_type = string + description = The inheritance models followed for the variant + category = inheritance_models + field = INFO + info_key = GeneticModels + record_rule = max + separators = ',', ':', '|', + + [[ad]] + priority = 1 + score = 3 + string = 'AD' + + [[ad_dn]] + priority = 1 + score = 3 + string = 'AD_dn' + + [[ar]] + priority = 1 + score = 3 + string = 'AR_hom' + + [[ar_dn]] + priority = 1 + score = 3 + string = 'AR_hom_dn' + + [[ar_comp]] + priority = 1 + score = 3 + string = 'AR_comp' + + [[ar_comp_dn]] + priority = 1 + score = 3 + string = 'AR_comp_dn' + + [[xr]] + priority = 1 + score = 3 + string = 'XR' + + [[xr_dn]] + priority = 1 + score = 3 + string = 'XR_dn' + + [[xd]] + priority = 1 + score = 3 + string = 'XD' + + [[xd_dn]] + priority = 1 + score = 3 + string = 'XD_dn' + + [[not_reported]] + score = 0 + +[model_score] + category = variant_call_quality_filter + data_type = integer + description = The inheritance model score + field = INFO + info_key = ModelScore + record_rule = min + separators = ',',':', + + [[not_reported]] + score = 0 + + [[low_qual]] + score = -5 + lower = 0 + upper = 20 + + [[high_qual]] + score = 0 + lower = 20 + upper = 300 + [most_severe_consequence] category = consequence data_type = string