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 — System design

• Input Formats — File specifications