Glossary

AC (Allele Count)

Number of copies of the alternate allele observed across eligible samples. A heterozygous carrier contributes 1; a homozygous alt carrier contributes 2. See Key Concepts.

AF (Allele Frequency)

Ratio of AC to AN (AC / AN). Represents the proportion of alleles that are the alternate allele among eligible samples. Returns None when AN=0. See Key Concepts.

AN (Allele Number)

Total number of alleles examined across eligible samples. For autosomes, AN = 2 × number of eligible diploid samples. For sex chromosomes, AN depends on ploidy. See Ploidy & Sex Chromosomes.

Bitmap

See Roaring Bitmap.

Bucket

A 1 Mbp (1,000,000 base pair) genomic interval used to partition variant data within each chromosome. Bucket 0 covers positions 0–999,999; bucket 1 covers 1,000,000–1,999,999; and so on. See Data Model.

Carrier

A sample that has at least one copy of the alternate allele at a given position (heterozygous or homozygous alt). Use variant-info to list carriers with their metadata. See Variant Info.

Capture Index

An interval tree (stored as a .pkl file) built from a BED file that defines the genomic regions covered by a whole-exome sequencing (WES) technology. Used to determine which WES samples are eligible at a given position. WGS samples do not require a capture index. See Key Concepts.

Eligible Sample

A sample that passes all query filters (sex, phenotype, technology) and has coverage at the queried position. Only eligible samples contribute to AC and AN. See Sample Filtering.

N_FAIL

The count of eligible samples at a position where the genotype call had FILTER≠PASS in the source VCF. These samples are not counted in AC/AN. See FILTER=PASS Tracking.

Manifest

A TSV file that maps each sample to its VCF path, sex, sequencing technology, and phenotype codes. The manifest drives database creation and is parsed into metadata.sqlite. See Manifest Format.

Metadata Code

Legacy term. See Phenotype Code.

Parquet

A columnar storage format used by AFQuery to store variant bitmaps on disk. Each Parquet file covers one bucket within one chromosome and contains rows sorted by (pos, alt). See Data Model.

Phenotype Code

An arbitrary string label assigned to a sample in the manifest (e.g., ICD-10 codes, HPO terms, project tags). Multiple codes per sample are supported. Phenotype codes enable cohort stratification at query time. See Key Concepts.

Ploidy

The number of allele copies at a given locus, which depends on chromosome type and sex. Autosomes are diploid (ploidy=2) for all samples. chrX non-PAR is haploid for males, diploid for females. See Ploidy & Sex Chromosomes.

Roaring Bitmap

A compressed bitset data structure that efficiently stores sets of integers. AFQuery uses Roaring Bitmaps (via the pyroaring library) to represent which samples carry a given genotype. Typical compression: ~2 bytes per sample per variant. See roaringbitmap.org.

Schema Version

The AFQuery database format version stored in manifest.json. Each variant stores het_bitmap, hom_bitmap, and fail_bitmap. See Data Model.

Technology

The sequencing platform or assay type assigned to a sample (e.g., wgs, wes_v1, panel_cardiac). Determines capture index eligibility and enables technology-stratified queries. See Technology Integration.