Add sequence context and transcript information to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome

Usage

justify_id_vcf(
  ID.vcf,
  ref.genome,
  name.of.VCF = NULL,
  suppress.discarded.variants.warnings = TRUE,
  explain_indels = 1,
  context_width_multiplier = 20L
)

Arguments

ID.vcf: An in-memory ID (insertion/deletion) VCF as a data.frame. This function expects that there is a "context base" to the left, for example REF = ACG, ALT = A (deletion of CG) or REF = A, ALT = ACC (insertion of CC).
ref.genome: Can be a string or a BSgenome. If a string, it should a well-known name for reference genome in BSgenome
name.of.VCF: Name of the VCF file.
suppress.discarded.variants.warnings: If TRUE, do warn when variants that cannot be processed are discarded.
explain_indels: If 0, do not explain, if 1, explain indels that were justified (via messages), if 2, generate messages for all indels.
context_width_multiplier: Used to guess how much sequence on each side of an indel is needed to categorize it.

Value

A list of elements:

annotated.vcf: The original VCF data frame in which POS, REF and ALT with new columns added to the input data frame:
- seq.context: The sequence embedding the variant.
- seq.context.width: The width of seq.context to the left of the indel
- pos_shift
discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.

Examples

# See tests/testthat/test_indel_classification.R for an end-to-end example
# against a real Strelka ID VCF.