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

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

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

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

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).

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

Status	Meaning
PASS	Variant validated against reference, ready for counting
PASS_WARN_REF_CORRECTED	REF allele ≥90% match; corrected to FASTA REF
PASS_WARN_HOMOPOLYMER_DECOMP	Variant spans a homopolymer; dual-counted with corrected allele (corrected won)
PASS_MULTI_ALLELIC	Variant overlaps another variant at the same locus; sibling ALT exclusion active
REF_MISMATCH	REF allele does not match the reference genome at the stated position
FETCH_FAILED	Could not fetch the reference region (chromosome not found, etc.)

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

Term	Definition
BAQ	Base Alignment Quality — heuristic quality downgrade near indels to prevent false calls
UMI	Unique Molecular Identifier — barcode for molecule-level deduplication
Genomic binning	Variant grouping by chromosome for cache-efficient counting (`count_bam_binned`)
Parity test	Test verifying `count_bam` and `count_bam_binned` produce identical results
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`. Routed to `check_complex` instead of `check_deletion`.
has_nearby_length_match	Flag set in `check_deletion` when a windowed Del matches in length (≥5bp) but fails S3 sequence validation. Triggers Phase 3 SW fallback to handle BWA left-alignment shifts.
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.
is_worth_realignment	Predicate in `check_complex` 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.