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Annotate an in-memory ID (indel) VCF with sequence context, transcript strand, and COSMIC / Koh indel categories

Source: R/annotate_id_vcf.R
annotate_id_vcf.Rd

Port of ICAMS's AnnotateIDVCF(). Justifies each indel against the reference genome, optionally annotates transcript strand, and categorizes each justified indel into the COSMIC 83, Koh 89, and Koh 476 schemes.

Usage

annotate_id_vcf(
  vcf,
  ref_genome,
  trans_ranges = NULL,
  name_of_vcf = NULL,
  suppress_discarded_variants_warnings = TRUE,
  explain_indels = 1,
  context_width_multiplier = 20L,
  add_transcript_ranges = TRUE
)

Arguments

vcf

An in-memory ID VCF as a data.frame / data.table. Expects a "context base" to the left of the indel, e.g. REF = "ACG", ALT = "A" (deletion of CG) or REF = "A", ALT = "ACC" (insertion of CC).

ref_genome

A BSgenome object or a character alias (e.g. "GRCh37", "GRCh38", "mm10").

trans_ranges

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

name_of_vcf

Optional name for the VCF, used only in warning / error messages.

suppress_discarded_variants_warnings

If TRUE, do not warn when variants that cannot be processed are discarded.

explain_indels

If 0, do not explain. If 1, emit messages for indels whose position was left-shifted by justification. If 2, emit messages for all indels.

context_width_multiplier

Multiplier used to guess how much flanking sequence (per side) is needed to categorize each indel.

add_transcript_ranges

If TRUE, annotate transcript strand when a transcript-ranges table is available.

Value

A list with:

  • annotated.vcf: the input VCF with new columns seq.context, seq.context.width, pos_shift, COSMIC_83, Koh_89, Koh_476, and (when transcript ranges are available) trans.strand / bothstrand.

  • discarded.variants: rows that could not be justified, or NULL if none were discarded.