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[Version]
version = 1.2
name = svrank_model
[Categories]
[[allele_frequency]]
category_aggregation = min
[[Gene_intolerance_prediction]]
category_aggregation = sum
[[Clinical_significance]]
category_aggregation = sum
[[Inheritance_Models]]
category_aggregation = min
[[Consequence]]
category_aggregation = max
[[Variant_call_quality_filter]]
category_aggregate = sum
[[variant_length]]
category_aggregation = min
[[variant_type]]
category_aggregation = min
[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
[decipher]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = decipherAF
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
[clingen_ngi]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = clingen_ngiAF
description = clingen ngi 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
[SVR1000G]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = right_1000GAF
description = 1000 genomes frequency SV right interval
[[not_reported]]
score = 4
[[common]]
score = -6
lower = 0.02
upper = 1.1
[[intermediate]]
score = 1
lower = 0.005
upper = 0.02
[[rare]]
score = 2
lower = 0
upper = 0.005
[SVL1000G]
field = INFO
data_type = float
category = allele_frequency
record_rule = max
separators = ',',
info_key = left_1000GAF
description = 1000 genomes frequency SV left interval
[[not_reported]]
score = 4
[[common]]
score = -6
lower = 0.02
upper = 1.1
[[intermediate]]
score = 1
lower = 0.005
upper = 0.02
[[rare]]
score = 2
lower = 0
upper = 0.005
[IMPRECISE]
field = INFO
data_type = flag
category = variant_type
record_rule = min
separators = ',',
info_key = IMPRECISE
description = The type of structural variant
[[IMPRECISE]]
score = 0
[[not_reported]]
score = 3
[SVLEN]
field = INFO
data_type = integer
category = variant_length
record_rule = min
separators = ',',
info_key = SVLEN
description = The length of the structural variant
[[not_reported]]
score = 0
[[long_pos]]
score = -3
lower = 1000001
upper = 100000000
[[long_neg]]
score = -3
lower = -100000000
upper = -1000001
[[medium_pos]]
score = 3
lower = 50001
upper = 1000000
[[medium_neg]]
score = 3
lower = -1000000
upper = -50001
[[short]]
score = 8
lower = -50000
upper = 50000
[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
[clingen_cgh_benign]
field = INFO
data_type = integer
category = Clinical_significance
record_rule = max
separators = None
info_key = clingen_cgh_benign
description = Clinical significance
[[not_reported]]
score = 0
[[benign]]
score = -12
value = 1
[clingen_cgh_pathogenic]
field = INFO
data_type = integer
category = Clinical_significance
record_rule = max
separators = None
info_key = clingen_cgh_pathogenic
description = Clinical significance
[[not_reported]]
score = 0
[[pathogenic]]
score = 12
value = 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
[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
[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'