Filtering Guide

VarAnnote provides a powerful filtering system with 13 operators and predefined filter sets.

Filter Operators

Basic Operators

equals - Exact match
not_equals - Not equal
contains - Contains substring
not_contains - Does not contain
starts_with - Starts with string
ends_with - Ends with string

Numeric Operators

greater_than - Greater than value
less_than - Less than value
greater_equal - Greater than or equal
less_equal - Less than or equal

Advanced Operators

regex - Regular expression match
in_list - Value in list
range - Value in range

Predefined Filter Sets

High Confidence Variants

from varannote.utils.filters import FilterSet

filter_set = FilterSet()
filter_set.add_predefined("high_confidence")

Rare Variants

filter_set.add_predefined("rare_variants")

Coding Variants

filter_set.add_predefined("coding_variants")

Custom Filters

Single Filter

from varannote.utils.filters import FilterRule

# Filter for pathogenic variants
pathogenic_filter = FilterRule(
    field="clinvar.significance",
    operator="equals",
    value="Pathogenic"
)

Multiple Filters

from varannote.utils.filters import FilterSet

filter_set = FilterSet()
filter_set.add_rule("clinvar.significance", "equals", "Pathogenic")
filter_set.add_rule("gnomad.af", "less_than", 0.01)

Filter Combinations

# AND combination (default)
filter_set = FilterSet(logic="AND")

# OR combination
filter_set = FilterSet(logic="OR")