ICAMS (version 2.1.2)

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

Description

Create ID (small insertion and deletion) catalog from ID VCFs

Usage

VCFsToIDCatalogs(
  list.of.vcfs,
  ref.genome,
  region = "unknown",
  flag.mismatches = 0
)

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".

flag.mismatches

Optional. If > 0, then if there are mismatches to references in the ID (insertion/deletion) VCF, generate messages showing the mismatched rows and continue. Otherwise stop if there are mismatched rows. See AnnotateIDVCF for more details.

Value

A list of two elements. 1st element is an S3 object containing an ID (small insertion and deletion) catalog with class "IndelCatalog". See as.catalog for more details. 2nd element is a list of further annotated VCFs.

Examples

# NOT RUN {
file <- c(system.file("extdata/Strelka-ID-vcf/",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.ID.vcfs <- ReadStrelkaIDVCFs(file)                      
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5",
 quietly = TRUE)) {
  catID <- VCFsToIDCatalogs(list.of.ID.vcfs, ref.genome = "hg19",
                            region = "genome")}
# }