ICAMS (version 3.0.11)

VCFsToIDCatalogs: Create ID (small insertions and deletions) catalog from ID VCFs

Description

Create ID (small insertions and deletions) catalog from ID VCFs

Usage

VCFsToIDCatalogs(
  list.of.vcfs,
  ref.genome,
  num.of.cores = 1,
  trans.ranges = NULL,
  region = "unknown",
  flag.mismatches = 0,
  return.annotated.vcfs = FALSE,
  suppress.discarded.variants.warnings = TRUE
)

Value

A list of elements:

• catalog: The ID (small insertions and deletions) catalog with attributes added. See as.catalog for details.

• 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.

• annotated.vcfs: Non-NULL only if return.annotated.vcfs = TRUE. A list of data frames which contain the original VCF's ID mutation rows with three additional columns seq.context.width, seq.context and ID.class added. The category assignment of each ID mutation in VCF can be obtained from ID.class column.

Arguments

list.of.vcfs

List of in-memory ID VCFs. The list names will be the sample ids in the output catalog.

ref.genome

A ref.genome argument as described in ICAMS.

num.of.cores

The number of cores to use. Not available on Windows unless num.of.cores = 1.

trans.ranges

Optional. If ref.genome specifies one of the BSgenome object

1. BSgenome.Hsapiens.1000genomes.hs37d5

2. BSgenome.Hsapiens.UCSC.hg38

3. BSgenome.Mmusculus.UCSC.mm10

then the function will infer trans.ranges automatically. Otherwise, user will need to provide the necessary trans.ranges. Please refer to TranscriptRanges for more details. If is.null(trans.ranges) do not add transcript range information.

region

A character string acting as a region identifier, one of "genome", "exome".

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 and an element discarded.variants will appear in the return value. See AnnotateIDVCF for more details.

return.annotated.vcfs

Logical. Whether to return the annotated VCFs with additional columns showing mutation class for each variant. Default is FALSE.

suppress.discarded.variants.warnings

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

ID classification

See https://github.com/steverozen/ICAMS/blob/v3.0.9-branch/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx for additional information on ID (small insertions and deletions) mutation classification.

See the documentation for Canonicalize1Del which first handles deletions in homopolymers, then handles deletions in simple repeats with longer repeat units, (e.g. CACACACA, see FindMaxRepeatDel), and if the deletion is not in a simple repeat, looks for microhomology (see FindDelMH).

See the code for unexported function CanonicalizeID and the functions it calls for handling of insertions.

Examples

file <- c(system.file("extdata/Strelka-ID-vcf/",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.ID.vcfs <- ReadAndSplitVCFs(file, variant.caller = "strelka")$ID
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5",
 quietly = TRUE)) {
  catID <- VCFsToIDCatalogs(list.of.ID.vcfs, ref.genome = "hg19",
                            region = "genome")}