Write mutation_data to a VCF file

Export your mutation_data to a VCF file for downstream applications.

Usage

write_vcf_from_mut(mutation_data, output_path = NULL)

Arguments

mutation_data

A data frame of a GRanges object containing your mutation data. This can be the output of import_mut_data, import_vcf_data, or filter_mut. Coordinates must be 1-based. Required columns are "contig", "start", "end", "ref", "alt", "sample", "alt_depth", "total_depth", and "ref_depth". Additional columns are allowed.

output_path

The directory where the VCF file should be written. Default is NULL, which will write the file to the current working directory.

Value

Writes a VCF file of mutations "mutation_output.vcf".

Examples

if (requireNamespace("MutSeqRData", quietly = TRUE)) {
  # Example data consists of 24 mouse bone marrow DNA samples imported
  # using import_mut_data() and filtered with filter_mut as in Example 4.
  # Sequenced on TS Mouse Mutagenesis Panel. Example data is
  # retrieved from MutSeqRData, an ExperimentHub data package.
  library(ExperimentHub)
  eh <- ExperimentHub()
  example_data <- eh[["EH9861"]]

  write_vcf_from_mut(mutation_data = example_data, output_path = tempdir())
}