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 |
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 |
| Smith-Waterman (SW) |
Default Phase 3 alignment backend. Uses edit-distance scoring to align reads against REF and ALT haplotypes. Confident call requires ≥2 score margin. |
| PairHMM |
Alternative Phase 3 alignment backend (--alignment-backend hmm). Uses pair hidden Markov model with base quality probabilities for probabilistic alignment scoring. |
| 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 |
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.) |
abbreviations