merge_vcf: merge_vcf

In nikopech/lineagespot: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

Description

Merge Variant Calling Format (VCF) files into a single tab-delimited table

Usage

merge_vcf(
  vcf_fls = NULL,
  vcf_folder = NULL,
  gff3_path = NULL,
  file.out = paste0("Variant_table_", Sys.Date(), ".txt"),
  print.out = FALSE
)

Arguments

vcf_fls	A list of paths to VCF files
vcf_folder	A path to a folder containing all VCF file that will be integrated into a single table
gff3_path	Path to GFF3 file
file.out	Given name for the output file
print.out	Logical value indicating if the produced table should be printed

Value

A data table contaiing all variants from each sample of the input VCF files

Examples

merge_vcf(vcf_folder = system.file("extdata",
                                   "vcf-files",
                                   package = "lineagespot"),

          gff3_path = system.file("extdata",
                                  "NC_045512.2_annot.gff3",
                                  package = "lineagespot"))

nikopech/lineagespot documentation built on Dec. 28, 2021, 12:15 a.m.