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Annotate an SBS or DBS VCF with flanking sequence context and transcript strand

Source: R/annotate_sbs_or_dbs_vcf.R
annotate_sbs_or_dbs_vcf.Rd

Adds flanking sequence context via add_seq_context() and, when a transcript-ranges table is available, transcript strand via add_transcript_strand(). The same pipeline is appropriate for SBS and DBS; DBS-specific validation (e.g. no N in the tetranucleotide context) happens downstream in vcf_to_dbs_catalog().

Usage

annotate_sbs_or_dbs_vcf(
  vcf,
  ref_genome,
  trans_ranges = NULL,
  seq_context_width = 10L,
  name_of_vcf = NULL
)

Arguments

vcf

A VCF as a data.frame / data.table with CHROM, POS, REF, ALT columns. For SBS, REF and ALT are single bases; for DBS, both are two bases.

ref_genome

A BSgenome object or a character alias accepted by normalize_genome_arg().

trans_ranges

Optional transcript-ranges data.table. If NULL, the shipped table is used when available for ref_genome.

seq_context_width

Width (per side) of the flanking-sequence window (default 10 → 21-base window).

name_of_vcf

Optional VCF name used in warnings.

Value

A list with:

  • annotated.vcf: the input VCF with new columns seq.<N>bases and (when transcript ranges are available) trans.strand / bothstrand.

  • discarded.variants: currently always NULL for this path (included for symmetry with annotate_id_vcf()).