VarAnnote
User Guide:
Installation Guide
Quick Start Guide
Configuration Guide
CLI Usage Guide
Filtering Guide
Output Formats Guide
Changelog
API Reference:
Annotator API
Databases API
Configuration Manager API
Filters API
VarAnnote
Index
Index
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A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
_
__init__() (varannote.core.annotator.VariantAnnotator method)
(varannote.databases.clinvar.ClinVarDatabase method)
(varannote.databases.cosmic.COSMICDatabase method)
(varannote.databases.dbsnp.DbSNPDatabase method)
(varannote.databases.gnomad.GnomADDatabase method)
(varannote.tools.annotator.VariantAnnotatorTool method)
(varannote.utils.config_manager.CacheConfig method)
(varannote.utils.config_manager.ConfigManager method)
(varannote.utils.config_manager.DatabaseConfig method)
(varannote.utils.config_manager.LoggingConfig method)
(varannote.utils.config_manager.OutputConfig method)
(varannote.utils.config_manager.PerformanceConfig method)
(varannote.utils.filters.FilterRule method)
(varannote.utils.filters.FilterSet method)
(varannote.utils.filters.VariantFilter method)
A
annotate_batch() (varannote.core.annotator.VariantAnnotator method)
annotate_file() (varannote.tools.annotator.VariantAnnotatorTool method)
api_key (varannote.utils.config_manager.DatabaseConfig attribute)
apply_clinical_filter() (in module varannote.utils.filters)
apply_filter() (varannote.utils.filters.VariantFilter method)
apply_multiple_filters() (varannote.utils.filters.VariantFilter method)
apply_predefined_filter() (in module varannote.utils.filters)
apply_quality_filter() (in module varannote.utils.filters)
available_formats (varannote.utils.config_manager.OutputConfig attribute)
B
backup_count (varannote.utils.config_manager.LoggingConfig attribute)
batch_annotate() (varannote.databases.clinvar.ClinVarDatabase method)
(varannote.databases.cosmic.COSMICDatabase method)
(varannote.databases.dbsnp.DbSNPDatabase method)
(varannote.databases.gnomad.GnomADDatabase method)
batch_size (varannote.utils.config_manager.PerformanceConfig attribute)
BENIGN (varannote.utils.filters.ClinicalSignificance attribute)
C
cache_cleanup_interval (varannote.utils.config_manager.PerformanceConfig attribute)
CacheConfig (class in varannote.utils.config_manager)
categories (varannote.utils.config_manager.LoggingConfig attribute)
ClinicalSignificance (class in varannote.utils.filters)
ClinVarDatabase (class in varannote.databases.clinvar)
compression (varannote.utils.config_manager.CacheConfig attribute)
ConfigManager (class in varannote.utils.config_manager)
CONFLICTING (varannote.utils.filters.ClinicalSignificance attribute)
CONTAINS (varannote.utils.filters.FilterOperator attribute)
COSMICDatabase (class in varannote.databases.cosmic)
create_clinical_filter() (varannote.utils.filters.VariantFilter method)
create_consequence_filter() (varannote.utils.filters.VariantFilter method)
create_custom_filter() (varannote.utils.filters.VariantFilter method)
create_gene_filter() (varannote.utils.filters.VariantFilter method)
create_quality_filter() (varannote.utils.filters.VariantFilter method)
D
DatabaseConfig (class in varannote.utils.config_manager)
DbSNPDatabase (class in varannote.databases.dbsnp)
default_format (varannote.utils.config_manager.OutputConfig attribute)
description (varannote.utils.filters.FilterRule attribute)
(varannote.utils.filters.FilterSet attribute)
directory (varannote.utils.config_manager.CacheConfig attribute)
(varannote.utils.config_manager.LoggingConfig attribute)
E
enabled (varannote.utils.config_manager.CacheConfig attribute)
(varannote.utils.config_manager.DatabaseConfig attribute)
(varannote.utils.filters.FilterSet attribute)
EQUALS (varannote.utils.filters.FilterOperator attribute)
export_config() (varannote.utils.config_manager.ConfigManager method)
F
field (varannote.utils.filters.FilterRule attribute)
FilterOperator (class in varannote.utils.filters)
FilterRule (class in varannote.utils.filters)
filters (varannote.utils.config_manager.OutputConfig attribute)
FilterSet (class in varannote.utils.filters)
G
get() (varannote.utils.config_manager.ConfigManager method)
get_annotation_summary() (varannote.tools.annotator.VariantAnnotatorTool method)
get_config() (in module varannote.utils.config_manager)
get_config_manager() (in module varannote.utils.config_manager)
get_config_summary() (varannote.utils.config_manager.ConfigManager method)
get_database_config() (in module varannote.utils.config_manager)
(varannote.utils.config_manager.ConfigManager method)
get_database_info() (varannote.databases.clinvar.ClinVarDatabase method)
(varannote.databases.cosmic.COSMICDatabase method)
(varannote.databases.dbsnp.DbSNPDatabase method)
(varannote.databases.gnomad.GnomADDatabase method)
get_enabled_databases() (in module varannote.utils.config_manager)
(varannote.utils.config_manager.ConfigManager method)
get_filter_statistics() (varannote.utils.filters.VariantFilter method)
get_functional_annotations() (varannote.core.annotator.VariantAnnotator method)
get_population_frequencies() (varannote.databases.gnomad.GnomADDatabase method)
get_predefined_filter() (varannote.utils.filters.VariantFilter method)
get_variant_annotation() (varannote.databases.clinvar.ClinVarDatabase method)
(varannote.databases.cosmic.COSMICDatabase method)
(varannote.databases.dbsnp.DbSNPDatabase method)
(varannote.databases.gnomad.GnomADDatabase method)
get_variant_filter() (in module varannote.utils.filters)
GnomADDatabase (class in varannote.databases.gnomad)
GREATER_EQUAL (varannote.utils.filters.FilterOperator attribute)
GREATER_THAN (varannote.utils.filters.FilterOperator attribute)
I
IN (varannote.utils.filters.FilterOperator attribute)
include_fields (varannote.utils.config_manager.OutputConfig attribute)
IS_NOT_NULL (varannote.utils.filters.FilterOperator attribute)
IS_NULL (varannote.utils.filters.FilterOperator attribute)
L
LESS_EQUAL (varannote.utils.filters.FilterOperator attribute)
LESS_THAN (varannote.utils.filters.FilterOperator attribute)
level (varannote.utils.config_manager.LoggingConfig attribute)
LIKELY_BENIGN (varannote.utils.filters.ClinicalSignificance attribute)
LIKELY_PATHOGENIC (varannote.utils.filters.ClinicalSignificance attribute)
list_predefined_filters() (varannote.utils.filters.VariantFilter method)
LoggingConfig (class in varannote.utils.config_manager)
logic (varannote.utils.filters.FilterSet attribute)
M
main() (in module varannote.tools.annotator)
max_age_days (varannote.utils.config_manager.CacheConfig attribute)
max_cache_size_mb (varannote.utils.config_manager.PerformanceConfig attribute)
max_concurrent_requests (varannote.utils.config_manager.PerformanceConfig attribute)
max_connections (varannote.utils.config_manager.PerformanceConfig attribute)
max_connections_per_host (varannote.utils.config_manager.PerformanceConfig attribute)
max_file_size_mb (varannote.utils.config_manager.LoggingConfig attribute)
max_size_gb (varannote.utils.config_manager.CacheConfig attribute)
max_workers (varannote.utils.config_manager.PerformanceConfig attribute)
module
varannote.core.annotator
varannote.databases.clinvar
varannote.databases.cosmic
varannote.databases.dbsnp
varannote.databases.gnomad
varannote.tools.annotator
varannote.utils.config_manager
varannote.utils.filters
N
name (varannote.utils.config_manager.DatabaseConfig attribute)
(varannote.utils.filters.FilterSet attribute)
NOT_CONTAINS (varannote.utils.filters.FilterOperator attribute)
NOT_EQUALS (varannote.utils.filters.FilterOperator attribute)
NOT_IN (varannote.utils.filters.FilterOperator attribute)
NOT_PROVIDED (varannote.utils.filters.ClinicalSignificance attribute)
O
operator (varannote.utils.filters.FilterRule attribute)
OutputConfig (class in varannote.utils.config_manager)
P
PATHOGENIC (varannote.utils.filters.ClinicalSignificance attribute)
PerformanceConfig (class in varannote.utils.config_manager)
priority (varannote.utils.config_manager.DatabaseConfig attribute)
R
rate_limit (varannote.utils.config_manager.DatabaseConfig attribute)
REGEX (varannote.utils.filters.FilterOperator attribute)
rules (varannote.utils.filters.FilterSet attribute)
S
save_user_config() (varannote.utils.config_manager.ConfigManager method)
set() (varannote.utils.config_manager.ConfigManager method)
strategies (varannote.utils.config_manager.CacheConfig attribute)
T
timeout (varannote.utils.config_manager.DatabaseConfig attribute)
U
UNCERTAIN_SIGNIFICANCE (varannote.utils.filters.ClinicalSignificance attribute)
use_parallel (varannote.utils.config_manager.PerformanceConfig attribute)
V
value (varannote.utils.filters.FilterRule attribute)
varannote.core.annotator
module
varannote.databases.clinvar
module
varannote.databases.cosmic
module
varannote.databases.dbsnp
module
varannote.databases.gnomad
module
varannote.tools.annotator
module
varannote.utils.config_manager
module
varannote.utils.filters
module
VariantAnnotator (class in varannote.core.annotator)
VariantAnnotatorTool (class in varannote.tools.annotator)
VariantFilter (class in varannote.utils.filters)