abbreviations

*[VAF]: Variant Allele Frequency - Fraction of reads supporting the variant allele *[MAF]: Mutation Annotation Format - Standard mutation annotation file format *[VCF]: Variant Call Format - Standard variant call file format *[BAM]: Binary Alignment Map - Compressed sequence alignment file format *[BAI]: BAM Index - Index file for rapid BAM access *[FASTA]: FASTA format - Reference genome sequence file *[FAI]: FASTA Index - Index file for rapid FASTA access *[MAPQ]: Mapping Quality - Confidence score for read alignment *[BASEQ]: Base Quality - Phred-scaled base call confidence *[cfDNA]: Cell-free DNA - Circulating DNA fragments in blood plasma *[ctDNA]: Circulating tumor DNA - Tumor-derived cfDNA fragments *[HPC]: High-Performance Computing - Cluster computing environment *[SIF]: Singularity Image Format - Container image format for HPC *[TSV]: Tab-Separated Values - Plain text tabular data format *[GBCMS]: Get Base Count Multi Sample - Multi-BAM variant counting tool *[CLI]: Command Line Interface - Terminal-based program interface *[CI]: Continuous Integration - Automated build and test system *[CD]: Continuous Deployment - Automated release system