ICAMS (version 2.1.2)

StrelkaIDVCFFilesToCatalog: Create ID (small insertion and deletion) catalog from Strelka ID VCF files

Description

Create ID (small insertion and deletion) catalog from the Strelka ID VCFs specified by files

Usage

StrelkaIDVCFFilesToCatalog(
  files,
  ref.genome,
  region = "unknown",
  names.of.VCFs = NULL,
  flag.mismatches = 0
)

Arguments

files

Character vector of file paths to the Strelka ID VCF files.

ref.genome

A ref.genome argument as described in ICAMS.

region

A character string designating a genomic region; see as.catalog and ICAMS.

names.of.VCFs

Optional. Character vector of names of the VCF files. The order of names in names.of.VCFs should match the order of VCF file paths in files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.

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.

Details

This function calls VCFsToIDCatalogs

Examples

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