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[Version]
version = 1.20
name = rank_model_cmms
[Categories]
[[allele_frequency]]
category_aggregation = min
[[Protein_prediction]]
category_aggregation = sum
[[Gene_intolerance_prediction]]
category_aggregation = max
[[Inheritance_Models]]
category_aggregation = min
[[Consequence]]
category_aggregation = max
[[Conservation]]
category_aggregation = sum
[[Variant_call_quality_filter]]
category_aggregation = sum
[[Deleteriousness]]
category_aggregation = max
[[Clinical_significance]]
category_aggregation = sum
[[Splicing]]
category_aggregation = min
[Spidex]
field = INFO
data_type = float
category = Splicing
record_rule = max
separators = ',',
info_key = SPIDEX
description = The Spidex z score
[[not_reported]]
score = 0
[[low]]
score = 0
lower = -1
upper = 1
[[medium_pos]]
score = 3
lower = 1
upper = 2
[[medium_neg]]
score = 3
lower = -2
upper = -1
[[high_pos]]
score = 5
lower = 2
upper = 100
[[high_neg]]
score = 5
lower = -100
upper = -2
[Model_score]
field = INFO
data_type = integer
category = Variant_call_quality_filter
record_rule = min
separators = ',',':',
info_key = ModelScore
description = The inheritance model score
[[not_reported]]
score = 0
[[low_qual]]
score = -5
lower = 0
upper = 20
[[high_qual]]
score = 0
lower = 20
upper = 300
[1000G]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = 1000GAF
description = 1000 genomes frequency
[[not_reported]]
score = 4
[[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 = 3
lower = 0
upper = 0.0005
[Swegen]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = SWEGENAF
description = Swegen genomes frequency
[[not_reported]]
score = 4
[[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 = 3
lower = 0
upper = 0.0005
[GNOMAD]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = GNOMADAF_POPMAX
description = GnomAD frequency
[[not_reported]]
score = 4
[[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 = 3
lower = 0
upper = 0.0005
[MTAF]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = MTAF
description = genbank MT frequency
[[not_reported]]
score = 4
[[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 = 3
lower = 0
upper = 0.0005
[LOCUSDB]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = Obs
description = LocusDb observation count
[[not_reported]]
score = 4
[[common]]
score = -12
lower = 20
upper = 10000000
[[intermediate]]
score = 1
lower = 10
upper = 20
[[rare]]
score = 2
lower = 5
upper = 10
[[very_rare]]
score = 3
lower = 1
upper = 5
[PolyPhen]
field = INFO
data_type = string
category = Protein_prediction
record_rule = max
info_key = CSQ
csq_key = PolyPhen
separators = None
description = The polyphen prediction
[[not_reported]]
score = 0
[[probably_damaging]]
score = 1
priority = 3
string = 'probably_damaging'
[[possibly_damaging]]
score = 1
priority = 2
string = 'possibly_damaging'
[[bening]]
score = 0
priority = 1
string = 'benign'
[Sift]
field = INFO
data_type = string
category = Protein_prediction
record_rule = max
separators = None
info_key = CSQ
csq_key = SIFT
description = The polyphen prediction
[[not_reported]]
score = 0
[[deleterious]]
score = 1
priority = 2
string = 'deleterious'
[[tolerated]]
score = 0
priority = 1
string = 'tolerated'
[Gene_intolerance_score]
field = INFO
data_type = float
category = Gene_intolerance_prediction
record_rule = max
separators = None
info_key = CSQ
csq_key = LoFtool
description = Exac gene intolerance prediction
[[not_reported]]
score = 0
[[low]]
score = 2
lower = 0
upper = 0.0001
[[medium_pos]]
score = 1
lower = 0.0001
upper = 0.01
[[high_pos]]
score = 0
lower = 0.01
upper = 1
[GeneticModels]
field = INFO
data_type = string
category = Inheritance_Models
record_rule = max
separators = ',', ':', '|',
info_key = GeneticModels
description = The inheritance models followed for the variant
[[ad]]
priority = 1
score = 1
string = 'AD'
[[ad_dn]]
score = 1
priority = 1
string = 'AD_dn'
[[ar]]
score = 1
priority = 1
string = 'AR_hom'
[[ar_dn]]
score = 1
priority = 1
string = 'AR_hom_dn'
[[ar_comp]]
score = 1
priority = 1
string = 'AR_comp'
[[ar_comp_dn]]
score = 1
priority = 1
string = 'AR_comp_dn'
[[xr]]
score = 1
priority = 1
string = 'XR'
[[xr_dn]]
score = 1
priority = 1
string = 'XR_dn'
[[xd]]
score = 1
priority = 1
string = 'XD'
[[xd_dn]]
score = 1
priority = 1
string = 'XD_dn'
[[not_reported]]
score = -12
[most_severe_consequence]
field = INFO
data_type = string
category = Consequence
record_rule = max
separators = ',', ':', '|',
info_key = most_severe_consequence
description = The most severe consequence for this variant
[[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'
[[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'
[[coding_sequence_variant]]
score = 1
priority = 2
string = 'coding_sequence_variant'
[[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]
field = FILTER
data_type = string
category = Variant_call_quality_filter
record_rule = min
separators = ';',
description = The filters for the variant
[[not_reported]]
score = 0
[[pass]]
score = 3
priority = 1
string = 'PASS'
[dbNSFP_GERP++_RS]
field = INFO
data_type = float
category = Conservation
record_rule = max
separators = ',',
info_key = dbNSFP_GERP___RS
description = Gerp conservation score
[[not_reported]]
score = 0
[[conserved]]
score = 1
lower = 2
upper = 10
[[not_conserved]]
score = 0
lower = 0
upper = 2
[dbNSFP_phastCons100way_vertebrate]
field = INFO
data_type = float
category = Conservation
record_rule = max
separators = ',',
info_key = dbNSFP_phastCons100way_vertebrate
description = phastCons conservation score
[[not_reported]]
score = 0
[[conserved]]
score = 1
lower = 0.8
upper = 100
[[not_conserved]]
score = 0
lower = 0
upper = 0.8
[dbNSFP_phyloP100way_vertebrate]
field = INFO
data_type = float
category = Conservation
record_rule = max
separators = ',',
info_key = dbNSFP_phyloP100way_vertebrate
description = Phylop conservation score
[[not_reported]]
score = 0
[[conserved]]
score = 1
lower = 2.5
upper = 100
[[not_conserved]]
score = 0
lower = 0
upper = 2.5
[CADD]
field = INFO
data_type = float
category = Deleteriousness
record_rule = max
separators = ',',
info_key = CADD
description = The CADD deleterious score
[[not_reported]]
score = 0
[[low]]
score = 0
lower = 0
upper = 10
[[medium]]
score = 2
lower = 10
upper = 20
[[high]]
score = 3
lower = 20
upper = 30
[[higher]]
score = 4
lower = 30
upper = 40
[[highest]]
score = 5
lower = 40
upper = 100
[CLNSIG]
field = INFO
data_type = float
category = Clinical_significance
record_rule = max
separators = '|',
info_key = CLNSIG
description = Clinical significance
[[not_reported]]
score = 0
[[not_provided]]
score = 0
value = 1
[[benign]]
score = -1
value = 2
[[likely_benign]]
score = 0
value = 3
[[uncertain_significance]]
score = 0
value = 0
[[drug_response]]
score = 0
value = 6
[[histocompatibility]]
score = 0
value = 7
[[other]]
score = 0
value = 255
[[likely_pathogenic]]
score = 2
value = 4
[[pathogenic]]
score = 5
value = 5
[CLNREVSTAT]
field = INFO
data_type = string
category = Clinical_significance
record_rule = max
separators = ',',
info_key = CLNREVSTAT
description = Clinical_review_status
[[not_reported]]
score = 0
[[no_assertion]]
score = 0
priority = 0
string = 'no_assertion'
[[no_criteria]]
score = 0
priority = 0
string = 'no_criteria'
[[single]]
score = 1
priority = 1
string = 'single'
[[conf]]
score = 1
priority = 1
string = 'conf'
[[mult]]
score = 2
priority = 2
string = 'mult'
[[exp]]
score = 3
priority = 3
string = 'exp'
[[guideline]]
score = 4
priority = 4
string = 'guideline'