ICAMS (version 2.0.7)

StrelkaIDVCFFilesToCatalog: Create ID (indel) catalog from Strelka ID VCF files

Description

Create ID (indel) catalog from the Strelka ID VCFs specified by files

Usage

StrelkaIDVCFFilesToCatalog(files, ref.genome, region = "unknown")

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.

Value

An ID (indel) catalog with attributes added. See as.catalog for more details.

Details

This function calls VCFsToIDCatalogs

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.ID.GRCh37.vcf",
                      package = "ICAMS"))
catID <- StrelkaIDVCFFilesToCatalog(file, ref.genome = "hg19", 
                                          region = "genome")
# }