Index

_

_default_acmg_scores (in module charger.config)

_default_charger_scores (in module charger.config)

A

acmg_decisions (CharGerResult attribute) acmg_module_scores (CharGerConfig attribute) ACMG_MODULES (in module charger.config) ACTIVE (ModuleAvailability attribute) ALL_CONSEQUENCE_TYPES (in module charger.csq)

ALL_INFRAME_TYPES (in module charger.csq) ALL_TRUNCATION_TYPES (in module charger.csq) alt_allele (Variant attribute) AUTO_DOMINANT (GeneInheritanceMode attribute) AUTO_RECESSIVE (GeneInheritanceMode attribute)

B

BA1 BENIGN (ClinicalSignificance attribute) BP1 BP1_gene_list (CharGerConfig attribute) bp1_genes (CharGer attribute) BP2 BP3

BP4 BP5 BP6 BP7 BS1 BS2 BS3 BS4

C

CharGer (class in charger.classifier) charger.acmg_modules module charger.acmg_modules.pathogenic module charger.argtype module charger.console module charger.custom_modules module charger.custom_modules.pathogenic module

charger_decisions (CharGerResult attribute) charger_module_scores (CharGerConfig attribute) CHARGER_MODULES (in module charger.config) CharGerConfig (class in charger.config) CharGerResult (class in charger.result) chrom (Variant attribute) ClinicalSignificance (class in charger.variant) clinvar (CharGerResult attribute) clinvar_table (CharGerConfig attribute) common_threshold (CharGerConfig attribute) config (CharGer attribute) consequence_types (CSQ property) create_console_parser() (in module charger.console) CSQ (class in charger.csq)

D

data (CSQ attribute)

delimiter (unix_tab attribute) disease_specific (CharGerConfig attribute)

E

end_pos (Variant attribute)

F

FAILED (ModuleDecision attribute)

filter (Variant attribute) from_cyvcf2() (Variant class method)

G

GeneInheritanceMode (class in charger.variant) get_most_severe_csq() (Variant method)

get_vep_csq_fields() (Variant class method) get_vep_version() (Variant class method)

H

hotspot3d_cluster (CharGerConfig attribute)

I

id (Variant attribute) include_vcf_details (CharGerConfig attribute) info (Variant attribute) inheritance_gene_table (CharGerConfig attribute) inheritance_genes (CharGer attribute) InheritanceGenesType (in module charger.classifier) input (CharGerConfig attribute)

input_variants (CharGer attribute) INVALID_SETUP (ModuleAvailability attribute) is_deletion() (Variant method) is_indel() (Variant method) is_inframe_type() (CSQ method) is_snp() (Variant method) is_sv() (Variant method) is_truncation_type() (CSQ method)

L

LIKELY_BENIGN (ClinicalSignificance attribute) LIKELY_PATHOGENIC (ClinicalSignificance attribute)

limit_seq_display() (in module charger.variant) lineterminator (unix_tab attribute)

M

max_benign_score (CharGerConfig attribute) max_likely_benign_score (CharGerConfig attribute) min_likely_pathogenic_score (CharGerConfig attribute) min_pathogenic_score (CharGerConfig attribute) module charger.acmg_modules charger.acmg_modules.pathogenic charger.argtype charger.console charger.custom_modules charger.custom_modules.pathogenic

ModuleAvailability (class in charger.classifier) ModuleDecision (class in charger.result) ModuleScoreOverrideType (class in charger.argtype)

O

output (CharGerConfig attribute)

override_variant_info (CharGerConfig attribute)

P

parse() (GeneInheritanceMode class method) parse_clinvar_record() (ClinicalSignificance class method) parse_console() (in module charger.console) parsed_csq (Variant attribute) PASSED (ModuleDecision attribute) PATHOGENIC (ClinicalSignificance attribute) pathogenic_variant (CharGerConfig attribute) pathogenic_variants (CharGer attribute) PathType (class in charger.argtype) PM1 PM2 PM3 PM4

PM5 PM6 PP1 PP2 PP2_gene_list (CharGerConfig attribute) pp2_genes (CharGer attribute) PP3 PP4 PP5 PS1 PS2 PS3 PS4 PVS1

R

rank_consequence_type() (CSQ method) rare_threshold (CharGerConfig attribute) read_and_parse_vcf() (Variant class method) read_csv() (in module charger.io) read_lines() (in module charger.io) read_tsv() (in module charger.io) read_vcf() (Variant class method) ref_allele (Variant attribute) REQUIRED_FIELDS (CSQ attribute) results (CharGer attribute)

run() (in module charger.console) run_acmg_modules() (CharGer method) run_charger_modules() (CharGer method) run_pm4() (in module charger.acmg_modules.pathogenic) run_pmc1() (in module charger.custom_modules.pathogenic) run_ppc1() (in module charger.custom_modules.pathogenic) run_ppc2() (in module charger.custom_modules.pathogenic) run_ps1() (in module charger.acmg_modules.pathogenic) run_psc1() (in module charger.custom_modules.pathogenic) run_pvs1() (in module charger.acmg_modules.pathogenic)

S

setup() (CharGer method)

setup_logger() (in module charger.console) start_pos (Variant attribute)

U

UNCERTAIN (ClinicalSignificance attribute)

unix_tab (class in charger.io) USER_DISABLED (ModuleAvailability attribute)

V

variant (CharGerResult attribute)

Variant (class in charger.variant)

X

X_LINKED_DOMINANT (GeneInheritanceMode attribute)

X_LINKED_RECESSIVE (GeneInheritanceMode attribute)

Y

Y_LINKED (GeneInheritanceMode attribute)