AnnotateIDVCF {ICAMS}

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

Description

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

Usage

AnnotateIDVCF(
  ID.vcf,
  ref.genome,
  flag.mismatches = 0,
  name.of.VCF = NULL,
  suppress.discarded.variants.warnings = TRUE
)

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

A ref.genome argument as described in ICAMS.

flag.mismatches

Deprecated. If there are ID variants whose REF do not match the extracted sequence from ref.genome, the function will automatically discard these variants. See element discarded.variants in the return value for more details.

name.of.VCF

Name of the VCF file.

suppress.discarded.variants.warnings

Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

Value

A list of elements:

• annotated.vcf: The original VCF data frame with two 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.

• 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

file <- c(system.file("extdata/Strelka-ID-vcf/",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMS"))
ID.vcf <- ReadStrelkaIDVCFs(file)[[1]]
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  list <- AnnotateIDVCF(ID.vcf, ref.genome = "hg19")
  annotated.ID.vcf <- list$annotated.vcf}