Read in the data lines of a Variant Call Format (VCF) file created by Mutect
ReadMutectVCF(file, name.of.VCF = NULL, tumor.col.name = NA)A data frame storing data lines of a VCF file with two additional columns added which contain the VAF(variant allele frequency) and read depth information.
The name/path of the VCF file, or a complete URL.
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.
Name or index of the column in VCF which contains the
tumor sample information. It must have quotation marks if
specifying the column name. If tumor.col.name is equal to
NA(default), this function will use the 10th column to calculate
VAFs. See GetMutectVAF for more details.