vcf2genoClasses: Convert VCF to genotypic classes

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Convert VCF to genotypic classes

Description

Convert genotypes at SNPs from a VCF file into genotypic classes.

Usage

vcf2genoClasses(
  vcf.file,
  genome = "",
  gclasses.file,
  ca.file,
  yieldSize = NA_integer_,
  dict.file = NULL,
  seq.id = NULL,
  seq.start = NULL,
  seq.end = NULL,
  na.string = NA,
  single.alt = TRUE,
  verbose = 1
)

Arguments

vcf.file	path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created)
genome	genome identifier (e.g. "VITVI_12x2")
gclasses.file	path to the output file to record genotypes into genotypic classes (will be gzipped if suffix is ".gz")
ca.file	path to the output file to record SNP 1-based coordinates and alleles (will be gzipped if suffix is ".gz")
yieldSize	number of records to yield each time the file is read from (see ?TabixFile) if seq.id is NULL
dict.file	path to the SAM dict file (see https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary) if seq.id is specified with no start/end
seq.id	see seqIdStartEnd2GRanges
seq.start	see seqIdStartEnd2GRanges
seq.end	see seqIdStartEnd2GRanges
na.string	a symbol to indicate missing genotypes (e.g. NA, "NN", "–", etc)
single.alt	if TRUE, only records with a single 'alt' are kept
verbose	verbosity level (0/1)

Value

invisible vector with the path to the output file

Author(s)

Gautier Sarah, Timothee Flutre

See Also

gtVcf2genoClasses, filterVariantCalls

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.