vivaldi (version 1.0.1)

arrange_data: arrange_data

Description

Reads in a directory of VCF files and converts them into a single dataframe

Usage

arrange_data(
  vardir,
  reference_fasta,
  annotated = "yes",
  ntlist = c("A", "G", "T", "C", "-"),
  verbose = FALSE
)

Value

A large dataframe containing information from all input VCF files

Arguments

vardir

Directory path containing vcf files

reference_fasta

Reference fasta file used for alignment

annotated

Whether the VCF files are annotated using snpeff "yes" or "no" (default "yes")

ntlist

Nucleotides (default A, T, G, C) used for finding multiple alt alleles

verbose

set verbosity of the vcfR commands