diff --git a/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini b/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini index d4f1cc6..ac3515f 100644 --- a/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini +++ b/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini @@ -191,23 +191,23 @@ [[common]] score = -12 - lower = 0.1 + lower = 0.02 upper = 1.1 [[intermediate]] - score = 0 - lower = 0.05 - upper = 0.1 + score = 1 + lower = 0.005 + upper = 0.02 [[rare]] score = 2 - lower = 0.01 - upper = 0.05 + lower = 0.0005 + upper = 0.005 [[very_rare]] score = 3 lower = 0 - upper = 0.01 + upper = 0.0005 [gene_intolerance_score] category = gene_intolerance_prediction @@ -302,7 +302,7 @@ [most_severe_consequence] category = consequence data_type = string - description = Most severe consequence for this variant (vep110) + description = Most severe consequence for this variant (vep107) field = INFO info_key = most_severe_consequence record_rule = max @@ -313,6 +313,11 @@ priority = 6 string = 'transcript_ablation' + [[feature_truncation]] + score = 8 + priority = 5 + string = 'feature_truncation' + [[splice_acceptor_variant]] score = 8 priority = 5 @@ -493,11 +498,6 @@ priority = 2 string = 'regulatory_region_variant' - [[feature_truncation]] - score = 1 - priority = 2 - string = 'feature_truncation' - [[intergenic_variant]] score = 0 priority = 0 @@ -719,20 +719,117 @@ [[common]] score = -12 - lower = 0.1 + lower = 0.02 upper = 1.1 [[intermediate]] - score = 0 - lower = 0.05 - upper = 0.1 + score = 1 + lower = 0.005 + upper = 0.02 [[rare]] score = 2 - lower = 0.01 - upper = 0.05 + lower = 0.0005 + upper = 0.005 [[very_rare]] score = 3 lower = 0 - upper = 0.01 \ No newline at end of file + upper = 0.0005 + +[revel] + category = protein_prediction + csq_key = REVEL_score + data_type = float + description = Revel score prediction + field = INFO + info_key = CSQ + record_rule = max + separators = None + + [[not_reported]] + score = 0 + + [[tolerated]] + score = 0 + lower = 0 + upper = 0.5 + + [[probably_damaging]] + score = 2 + lower = 0.5 + upper = 0.75 + + [[damaging]] + score = 5 + lower = 0.75 + upper = 1 + +[dbnsfp_gerp++_rs] + category = conservation + csq_key = GERP++_RS + data_type = float + description = Gerp conservation score + field = INFO + info_key = CSQ + record_rule = max + separators = ',', + + [[not_reported]] + score = 0 + + [[conserved]] + score = 1 + lower = 2 + upper = 10 + + [[not_conserved]] + score = 0 + lower = 0 + upper = 2 + +[dbnsfp_phastcons100way_vertebrate] + category = conservation + csq_key = phastCons100way_vertebrate + data_type = float + description = phastCons conservation score + field = INFO + info_key = CSQ + record_rule = max + separators = ',', + + [[not_reported]] + score = 0 + + [[conserved]] + score = 1 + lower = 0.8 + upper = 100 + + [[not_conserved]] + score = 0 + lower = 0 + upper = 0.8 + +[dbnsfp_phylop100way_vertebrate] + category = conservation + csq_key = phyloP100way_vertebrate + data_type = float + description = Phylop conservation score + field = INFO + info_key = CSQ + record_rule = max + separators = ',', + + [[not_reported]] + score = 0 + + [[conserved]] + score = 1 + lower = 2.5 + upper = 100 + + [[not_conserved]] + score = 0 + lower = 0 + upper = 2.5 \ No newline at end of file diff --git a/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini.md5 b/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini.md5 index 16c5551..988838c 100644 --- a/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini.md5 +++ b/nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini.md5 @@ -1 +1 @@ -9a8a11132c16243097f8295fa9606dc5 nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini +02ef4dcad483922461290865f9ca163b nallo/rank_model/grch38_rank_model_snvs_-v1.0-.ini diff --git a/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini b/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini index 04f63cf..31cf87d 100644 --- a/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini +++ b/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini @@ -37,32 +37,27 @@ separators = ',', [[not_reported]] - score = 4 - - [[missing]] - score = 4 - lower = -1 - upper = 0 + score = 6 [[common]] score = -12 - lower = 0.1 + lower = 0.02 upper = 1.1 [[intermediate]] - score = 0 - lower = 0.05 - upper = 0.1 + score = 1 + lower = 0.005 + upper = 0.02 [[rare]] score = 2 - lower = 0.01 - upper = 0.05 + lower = 0.0005 + upper = 0.005 [[very_rare]] - score = 3 + score = 4 lower = 0 - upper = 0.01 + upper = 0.0005 [colorsdb] category = allele_frequency @@ -74,32 +69,32 @@ separators = ',', [[not_reported]] - score = 4 + score = 6 [[missing]] - score = 4 + score = 6 lower = -1 upper = 0 [[common]] score = -12 - lower = 0.1 + lower = 0.05 upper = 1.1 [[intermediate]] - score = 0 - lower = 0.05 - upper = 0.1 + score = 1 + lower = 0.005 + upper = 0.05 [[rare]] score = 2 - lower = 0.01 - upper = 0.05 + lower = 0.0005 + upper = 0.005 [[very_rare]] - score = 3 + score = 4 lower = 0 - upper = 0.01 + upper = 0.0005 [loqusdb] category = allele_frequency @@ -111,32 +106,32 @@ separators = ',', [[not_reported]] - score = 4 + score = 6 [[missing]] - score = 4 + score = 6 lower = -1 upper = 0 - [[common]] + [[common]] score = -12 - lower = 0.1 + lower = 0.05 upper = 1.1 [[intermediate]] - score = 0 - lower = 0.05 - upper = 0.1 + score = 1 + lower = 0.005 + upper = 0.05 [[rare]] score = 2 - lower = 0.01 - upper = 0.05 + lower = 0.0005 + upper = 0.005 [[very_rare]] - score = 3 + score = 4 lower = 0 - upper = 0.01 + upper = 0.0005 [sv_len] category = variant_length @@ -180,6 +175,33 @@ lower = -400 upper = -1 +[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 + [genetic_models] data_type = string description = The inheritance models followed for the variant @@ -240,15 +262,14 @@ string = 'XD_dn' [[not_reported]] - score = 0 + score = 3 [most_severe_consequence] category = consequence data_type = string description = Most severe consequence for this variant (vep107) field = INFO - csq_key = Consequence - info_key = CSQ + info_key = most_severe_consequence record_rule = max separators = ',', ':', '|', @@ -257,6 +278,11 @@ priority = 6 string = 'transcript_ablation' + [[feature_truncation]] + score = 8 + priority = 5 + string = 'feature_truncation' + [[splice_acceptor_variant]] score = 8 priority = 5 @@ -437,11 +463,6 @@ priority = 2 string = 'regulatory_region_variant' - [[feature_truncation]] - score = 1 - priority = 2 - string = 'feature_truncation' - [[intergenic_variant]] score = 0 priority = 0 diff --git a/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini.md5 b/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini.md5 index 4670db2..4a39b05 100644 --- a/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini.md5 +++ b/nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini.md5 @@ -1 +1 @@ -da199871ea94f3f17ad7346f3e2c5dc9 nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini +eba620623e13d90796fab51902d1180d nallo/rank_model/grch38_rank_model_svs_-v1.0-.ini