ICAMS (version 3.0.11)

ReadVCFs: Read VCF files

Description

Read VCF files

Usage

ReadVCFs(
  files,
  variant.caller = "unknown",
  num.of.cores = 1,
  names.of.VCFs = NULL,
  tumor.col.names = NA,
  filter.status = DefaultFilterStatus(variant.caller),
  get.vaf.function = NULL,
  ...
)

Value

A list of data frames storing data lines of the VCF files with two additional columns added which contain the VAF(variant allele frequency) and read depth information.

Arguments

files

Character vector of file paths to the VCF files.

variant.caller

Name of the variant caller that produces the VCF, can be either "strelka", "mutect", "freebayes" or "unknown". This information is needed to calculate the VAFs (variant allele frequencies). If variant caller is "unknown"(default) and get.vaf.function is NULL, then VAF and read depth will be NAs. If variant caller is "mutect", do not merge SBSs into DBS.

num.of.cores

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

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.

tumor.col.names

Optional. Only applicable to Mutect VCFs. Vector of column names or column indices in Mutect VCFs which contain the tumor sample information. The order of elements in tumor.col.names should match the order of Mutect VCFs specified in files. If tumor.col.names is equal to NA(default), this function will use the 10th column in all the Mutect VCFs to calculate VAFs. See GetMutectVAF for more details.

filter.status

The character string in column FILTER of the VCF that indicates that a variant has passed all the variant caller's filters. Variants (lines in the VCF) for which the value in column FILTER does not equal filter.status are silently excluded from the output. The internal function DefaultFilterStatus tries to infer filter.status based on variant.caller. If variant.caller is "unknown", user must specify filter.status explicitly. If filter.status = NULL, all variants are retained. If there is no FILTER column in the VCF, all variants are retained with a warning.

get.vaf.function

Optional. Only applicable when variant.caller is "unknown". Function to calculate VAF(variant allele frequency) and read depth information from original VCF. See GetMutectVAF as an example. If NULL(default) and variant.caller is "unknown", then VAF and read depth will be NAs.

...

Optional arguments to get.vaf.function.

Examples

file <- c(system.file("extdata/Mutect-vcf",
                      "Mutect.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadVCFs(file, variant.caller = "mutect")