vcf_format_utils | R Documentation |
Format vcf files as alternative formats without going through a
snpRdata
intermediate. Used for working with likelihoods,
probabilities, or other non-GT format fields.
vcf2beagle(file, outfile)
vcf2pl(file, outfile, init_admix = FALSE, k = NULL)
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 |
k |
integer vector, default NULL. Numbers of ancestry clusters
(*k* values)for which to estimate intial admixture proportions for the
program |
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.
vcf2beagle()
: Format as a "beagle" likelihood file.
vcf2pl()
: Format as a "mgpl" phred-scaled likelihood file.
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