Glossary

Technical terms used throughout the documentation.

Metrics

Term	Definition
DP	Total depth — all mapped, quality-filtered reads overlapping the variant anchor position, including REF, ALT, and 'neither'. DP ≥ RD + AD.
VAF	Variant Allele Frequency — AD / (RD + AD)
Strand Bias	Fisher's exact test for read direction imbalance
AD	Alternate allele depth (supporting reads)
RD	Reference allele depth
Informative read	For an indel, a read that covers a flank of the event's shift-equivalence region and runs one base past the first base where REF and ALT differ. Only informative reads count REF; an ALT read that is not informative counts only when its own bases discriminate (a truncated long insertion's carrier does). The others count toward DP only (details).

File Formats

Term	Definition
VCF	Variant Call Format — standard variant file
MAF	Mutation Annotation Format — annotation-rich variant file
BAM	Binary Alignment Map — compressed alignment file
BAI	BAM Index — enables random access to BAM
FASTA	Reference genome sequence file
FAI	FASTA Index — enables random access to FASTA

Quality Scores

Term	Definition
MAPQ	Mapping Quality — confidence in read alignment
BASEQ	Base Quality — confidence in base call

cfDNA Terms

Term	Definition
cfDNA	Cell-free DNA — circulating DNA in plasma
ctDNA	Circulating tumor DNA — tumor-derived cfDNA
Duplex	Reads from both strands of original molecule

Alignment Backends

Term	Definition
PairHMM	Default Phase 3 alignment backend for all modes. Uses pair hidden Markov model with base quality probabilities for probabilistic alignment scoring. Selected via --alignment-backend pairhmm.
Smith-Waterman (SW)	Alternative Phase 3 alignment backend. Uses edit-distance scoring to align reads against REF and ALT haplotypes. Confident call requires ≥2 score margin. Selected via --alignment-backend sw.
LLR	Log-Likelihood Ratio — PairHMM confidence metric. LLR = ln(P(read|ALT)) - ln(P(read|REF)). Default threshold: 2.3 (≈ ln(10), i.e., 10:1 odds).

Fragment Metrics

Term	Definition
DPF	Fragment depth — total unique fragments (including discarded)
RDF	Reference fragment count — fragments resolved to REF
ADF	Alternate fragment count — fragments resolved to ALT
Fragment consensus	Quality-weighted method to resolve R1/R2 disagreements within a fragment

Validation Status

Status is two fields: gbcms_status (verdict PASS/FAIL) and gbcms_status_reason (|-separated reason tags, empty for a clean PASS).

The reasons and what each means: QC Flags → Verdict and status reasons.

RNA Terms

Term	Definition
Sense strand	mRNA coding strand; matches gene transcription direction
Antisense strand	Non-coding strand; template for transcription
A-to-I editing	Post-transcriptional RNA modification by ADAR enzymes; adenosine → inosine (read as guanosine)
NH tag	BAM tag indicating number of reported alignments for a read
Splice junction	CIGAR N operation representing an intron skip in RNA-seq reads
REDIportal	Database of known human A-to-I RNA editing sites

Engine Terms

Term	Definition
BAQ	Base Alignment Quality — heuristic quality downgrade (−20 BQ within 5 bp) near a read's insertions and deletions; a splice junction lowers none. Off by default for DNA (upstream BQSR), on by default for RNA (no upstream BQ calibration). See Read Filters: BAQ.
UMI	Unique Molecular Identifier — barcode for molecule-level deduplication
Genomic binning	Variant grouping by chromosome for cache-efficient counting (count_bam_binned)
Binning invariance	The rule that counts never depend on how variants are grouped into bins (window, cap, one variant per bin or per call); checked by tests/test_binning_invariance.py and every count_checked call
Read census	The tests' classification oracle (tests/census.py): each read judged by its own bases across the variant's tract
Complex Del+SNV	A deletion-format variant (len(REF) > len(ALT) == 1) where the anchor base also substitutes (alt[0] ≠ ref[0]). Examples: GC→T, AG→T. Judged by the exact-carrier rule instead of check_deletion.
Complex Ins+SNV	An insertion-format variant (len(REF) == 1 < len(ALT)) where the anchor base also substitutes (alt[0] ≠ ref[0]). Examples: C→TA, A→CCC. Judged by the exact-carrier rule instead of check_insertion (since 6.6.0, #121).
has_in_band_mismatch (removed in 6.7.0)	Flagged a large deletion (≥50bp) written with another length within 3bp whose deleted bases differed, for Phase-3 arbitration. Removed with the length band: a prepared deletion of 50bp or more is judged by its bases at the POS breakpoint (RJ-24), where another length is another allele.
has_shifted_same_length (removed in 6.6.0)	Routed a windowed same-length insertion of other bases to Phase-3 arbitration, whose closer haplotype let length win ALT and absorbed other alleles into REF. Such a read is now judged by its bases (RJ-21); the deletion side's in-band case is has_in_band_mismatch.
has_unreadable_insert	Flag set by the CIGAR checks for an insertion of the variant's length none of whose bases can be read (each N or below min_baseq, or the insert runs past the read end), at the anchor or inside the discrimination window: the read carries the length, not the sequence. On that path it is neither + partial_alt unless the variant is also written readably in the read; never Phase 3. The CIGAR checks judge only an insertion the exact-carrier rule cannot. Under that rule, which judges most insertions, such an insert inside the window is the ALT where no other allele of that length is at the locus (RJ-20, amended 2026-10-15). Written outside the window it is a separate event (RJ-8); it does not slide (RJ-21).
has_distinct_allele_nearby	Flag for a distinct-allele candidate in the scan window: a WRONG-length op (deletions only when ≥5bp — 1–4bp windowed Ds are alignment noise → plain REF; insertions at any size), the variant's inserted bases where they give another haplotype inside its discrimination window, or the variant written elsewhere with another change (gap, insertion, splice) across that window. Resolved without Phase 3: an indel of the read inside the discrimination window → neither + partial_alt (RJ-7); outside it a separate event → REF, no partial evidence (RJ-8).
another_allele_in_window	Flag for a windowed insertion of the variant's length, with a readable base of its own, that is not the ALT by its bases at any placement it can take and can sit inside the discrimination window, wherever the aligner wrote it (it slides a junction when the base it places onto the reference fits it), or whose fewest-mismatch placement, every junction it can reach scored by its readable mismatches, sits inside it (readable mismatches beside the insert block the slide; RJ-22): another allele there → neither + partial_alt, never REF or ALT (RJ-21, since 6.6.0).
left-alignment shift	BWA repositions an indel's anchor to the leftmost equivalent position. For partial-repeat regions, this places the anchor several bases left of where the CIGAR D operation appears in reads.
Exact carrier	A read whose own bases (soft clips included, bases below --min-baseq masked) carry the whole given allele of a complex variant with two reference flank bases each side, read at the event's own position. Only exact carriers count as REF or ALT for delins, Del+SNV and structural MNP reads. See the exact-carrier rule.
is_worth_realignment	Predicate in the previous complex classifier (check_complex, used only for a variant with no reference holding the event) returning true when a read's CIGAR contains indel evidence in the variant window. If false, M-block anchor coverage check classifies clean REF reads for deletion-direction variants.

Related

• Architecture — System design
• Input Formats — File specifications
• Complex Indels — Real-world case studies (Del+SNV, large DEL, shifted deletion)
• RNA CLI Reference — RNA-specific options