fRagmentomics

fRagmentomics characterizes cell-free DNA (cfDNA) fragments overlapping mutations of interest from aligned sequencing reads, outputting fragment size, 3' and 5' end sequences, and mutational status for each fragment.

Key Features:

• Multiple mutation input formats: Supports VCF, TSV, and string "chr:pos:ref:alt" representations.
• Genomic coordinate flexibility: Accommodates both one-based and zero-based genomic conventions.
• Mutation representation handling: Resolves mutation representation ambiguities.
• Reference genome compatibility: Accepts any reference file and species in FASTA format.
• Fragment feature extraction: Outputs fragment size, 3' end sequences, 5' end sequences, and mutational status for each cfDNA fragment.
• Optional variant normalization: Invokes bcftools norm to left-align and normalize variants when apply_bcftools_norm = TRUE.

Scientific Applications:

• CfDNA fragmentomic analysis: Enables characterization of cfDNA fragments at specific mutation sites for liquid biopsy research.
• Mutation-overlapping fragment profiling: Supports analysis of fragments overlapping one or multiple mutations of interest from BAM files.

Methodology:

fRagmentomics processes aligned reads from BAM files and characterizes cfDNA fragments overlapping specified mutations, with optional variant normalization via external bcftools norm.