ICAMS (version 2.0.8)

VCFsToIDCatalogs: Create ID (insertion and deletion) catalog from ID VCFs

Description

Create ID (insertion and deletion) catalog from ID VCFs

Usage

VCFsToIDCatalogs(list.of.vcfs, ref.genome, region = "unknown")

Arguments

list.of.vcfs

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

ref.genome

A ref.genome argument as described in ICAMS.

region

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

Value

An S3 object containing an ID (indel) catalog with class "catalog". See as.catalog for more details.

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
list.of.ID.vcfs <- ReadAndSplitMutectVCFs(file)$ID
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catID <- VCFsToIDCatalogs(list.of.ID.vcfs, ref.genome = "hg19",
                            region = "genome")}
# }