# Glossary

Technical terms used throughout the documentation.

## Metrics

| Term            | Definition                                       |
| --------------- | ------------------------------------------------ |
| **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                           |

## 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 |

## Related

* [Architecture](https://cmo-ci.gitbook.io/py-gbcms/reference/architecture) — System design
* [Input Formats](https://cmo-ci.gitbook.io/py-gbcms/reference/input-formats) — File specifications
