ReadVCFR Documentation

Read in the data lines of a Variant Call Format (VCF) file

Description

Read in the data lines of a Variant Call Format (VCF) file

Usage

ReadVCF(
  file,
  variant.caller = "unknown",
  name.of.VCF = NULL,
  tumor.col.name = NA,
  filter.status = NULL,
  get.vaf.function = NULL,
  ...
)

Arguments

file

The name/path of the VCF file, or a complete URL.

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 "unknown"(default) and get.vaf.function is NULL, then VAF and read depth will be NAs.

name.of.VCF

Name of the VCF file. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in file and file path without extensions (and the leading dot) will be used as the name of the VCF file.

tumor.col.name

Optional. Only applicable to Mutect VCF. Name of the column in Mutect VCF which contains the tumor sample information. It must have quotation marks. If tumor.col.name is equal to NA(default), this function will use the 10th column to calculate VAFs. See GetMutectVAF for more details.

filter.status

The status indicating a variant has passed all filters. An example would be "PASS". Variants which don't have the specified filter.status in the FILTER column in VCF will be removed. If NULL(default), no variants will be removed from the original VCF.

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.

num.of.cores

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

Value

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