vcf2phy: VCF format to Phylip format Converts VCF to phylip and saves...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

VCF format to Phylip format Converts VCF to phylip and saves the result to file. Output can be sequential or interleaved.

Description

VCF format to Phylip format

Converts VCF to phylip and saves the result to file. Output can be sequential or interleaved.

Usage

vcf2phy(
  x,
  save.as,
  missing = "-",
  sequential = TRUE,
  width = 300,
  padding = 5,
  partition.file = TRUE
)

Arguments

x	'vcfR' object (see package::vcfR) or character string with path to VCF file containing nucleotide data.
save.as	Path where phylip alignment should be saved
missing	Character to use for missing data in the output file. Default "-".
sequential	Whether or not data should be written on a single line (TRUE) or in multiple blocks (interleaced format) with the number of bases per line controlled by 'width'.
width	NULL or a number specifying the number of bases to write per line when output is interleaved.
padding	Number of spaces between the longest sample name and the first base.

Value

The value of 'save.as'.

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.