Glossary

Domain and tooling terms used throughout vflank. Acronyms also get hover tooltips wherever they appear in the docs (via the shared abbreviations list).

Assay & biology

ddPCR

Digital droplet PCR. The partitioned PCR assay that vflank's output is designed to feed: a primer/probe must bind a region free of patient/population variation, which is why flanks are masked.

Flank

The sequence immediately before (left) or after (right) a variant. vflank emits ±N reference bases around each variant, excluding the variant interval itself, as the design substrate for primers/probes.

Masking

Replacing a flank base with N so downstream design tools avoid it. vflank masks common population SNPs (gnomAD) and — with a BAM — patient-specific bases that disagree with the reference.

Fusion / junction

A chimeric sequence formed by joining two breakpoints from a structural variant. vflank builds the reverse-complement-aware junction so a probe can span it; the junction index marks where partner 2 begins.

Breakpoint

One side of a structural variant, given as chrom:pos:strand. Strand 0 is plus/reference, 1 is minus/complement (the iCallSV convention).

Variants & coordinates

MAF

Mutation Annotation Format. The primary small-variant input. Coordinates are 1-based, fully closed [start, end] — unlike pysam's 0-based half-open windows, the single most common source of off-by-one bugs (see Architecture).

VCF

Variant Call Format (1-based). Today vflank uses VCF only for population masking (gnomAD VCFs via --pop-vcf-dir); variant input is a MAF (small variants) or a breakpoint TSV (fusions). VCF as a variant-input format — small-variant VCF, and Delly CT/BND SV VCF — is a designed but unshipped direction (sv-vcf-input.md).

SNP

A single-nucleotide polymorphism common enough in the population to risk a primer/probe mismatch. Only single-base population SNPs are masked.

indel

An insertion or deletion. In the reference-frame consensus, deletions become N and insertion anchor sites are flagged N; true length-changing indel handling is the option-3 plan.

REF / ALT

The reference and alternate alleles. vflank shows the variant literally as [REF/ALT] between the two flanks in its FASTA output.

Population frequency (gnomAD)

gnomAD

The Genome Aggregation Database — vflank's source for population allele frequencies, queried either from a local VCF or the GraphQL API.

AF / AC / AN

Allele Frequency = Allele Count / Allele Number. A flank position is masked when its common-SNP AF clears the configured threshold (default 0.001).

Genome vs exome

gnomAD's two callsets. --pop-data {genome,exome,both} selects which to consult, symmetrically across the VCF and API backends.

Build (hg19/GRCh37, hg38/GRCh38)

The genome assembly. AF semantics differ across builds, so the build is explicit (-g, default hg19) and a mismatch warns rather than failing silently.

BAM consensus

BAM

A binary alignment file of a sample's reads. With --bam/--bam-map, vflank builds a per-sample patient consensus flank (masking modes C/D).

Consensus

The per-base call across a sample's reads, delegated to samtools consensus (bundled with pysam). Kept reference-length; a pure low-coverage overlay falls back to "patient where covered, population where blind."

CIGAR

A read's alignment string (M/I/D/N/S…). vflank walks CIGARs directly to flag insertions, because pysam's default pileup stepper silently drops reads on some sliced BAMs.

MQ / BQ

Mapping and base quality thresholds (--bam-min-mapq, --bam-min-baseq, default 20) gating which reads and bases count toward the consensus.

het / hom

Heterozygous / homozygous. A homozygous-ALT call corrects the flank base; a heterozygous position becomes N (or an IUPAC code with --bam-het-char iupac).

Low coverage

A position below --bam-min-depth (default 20). The default fallback is REF + gnomAD masking; --require-coverage instead flags the variant.

Downstream (out of scope for vflank)

Olivar

A small-variant amplicon designer. vflank produces its input; it does not design primers itself.

Primer3

A primer/probe designer used for fusion-junction probes. Same boundary: vflank emits the junction, Primer3 designs against it.