vcf_format_utils: Utilities for direct vcf file conversion

vcf_format_utilsR Documentation

Utilities for direct vcf file conversion

Description

Format vcf files as alternative formats without going through a snpRdata intermediate. Used for working with likelihoods, probabilities, or other non-GT format fields.

Usage

vcf2beagle(file, outfile)

vcf2pl(file, outfile, init_admix = FALSE, k = NULL)

Arguments

file

character, path to "vcf" file.

outfile

character, output filename.

init_admix

logical, default FALSE. If TRUE, will write initial admix estimates for the program entropy to a set of files for each k.

k

integer vector, default NULL. Numbers of ancestry clusters (*k* values)for which to estimate intial admixture proportions for the program entropy. Ignored if init_admix is FALSE.

Details

These functions are provided as a utility and do not work in the general snpR ecosystem. The different outputs may require specific FORMAT tags:

  • vcf2beagle: GP tag

  • vcf2PL: PL tag

If thes eare lacking, snpR may provide recommendations by which they can be added if possible.

Functions

  • vcf2beagle(): Format as a "beagle" likelihood file.

  • vcf2pl(): Format as a "mgpl" phred-scaled likelihood file.


hemstrow/snpR documentation built on Dec. 13, 2024, 4:27 a.m.