ReadAndSplitVCFs: Read and split VCF files

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Read and split VCF files

Description

Read and split VCF files

Usage

ReadAndSplitVCFs(
  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,
  ...,
  max.vaf.diff = 0.02,
  suppress.discarded.variants.warnings = TRUE,
  always.merge.SBS = FALSE,
  chr.names.to.process = NULL
)

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.
max.vaf.diff	Not applicable if variant.caller = "mutect". The maximum difference of VAF, default value is 0.02. If the absolute difference of VAFs for adjacent SBSs is bigger than max.vaf.diff, then these adjacent SBSs are likely to be "merely" asynchronous single base mutations, opposed to a simultaneous doublet mutation or variants involving more than two consecutive bases. Use negative value (e.g. -1) to suppress merging adjacent SBSs to DBS.
suppress.discarded.variants.warnings	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.
always.merge.SBS	If TRUE merge adjacent SBSs as DBSs regardless of VAFs and regardless of the value of max.vaf.diff and regardless of the value of get.vaf.function. It is an error to set this to TRUE when variant.caller = "mutect".
chr.names.to.process	A character vector specifying the chromosome names in VCF whose variants will be kept and processed, other chromosome variants will be discarded. If NULL(default), all variants will be kept except those on chromosomes with names that contain strings "GL", "KI", "random", "Hs", "M", "JH", "fix", "alt".

Value

A list containing the following objects:

• SBS: List of VCFs with only single base substitutions.

• DBS: List of VCFs with only doublet base substitutions.

• ID: List of VCFs with only small insertions and deletions.

• discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.

See Also

VCFsToCatalogs

Examples

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

ICAMS documentation built on June 15, 2025, 1:08 a.m.