vcf2dosage: Convert VCF to dose

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

Convert VCF to dose

Description

Convert genotypes at bi-allelic variants from a VCF file into allele doses. This is also doable with bcftools +dosage.

Usage

vcf2dosage(
  vcf.file,
  genome = "",
  gdose.file,
  ca.file,
  yieldSize = NA_integer_,
  dict.file = NULL,
  seq.id = NULL,
  seq.start = NULL,
  seq.end = NULL,
  field = "GT",
  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")
gdose.file	path to the output file to record genotypes as allele doses (will be gzipped); variants will be in rows and samples in columns
ca.file	path to the output file to record SNP 1-based coordinates and alleles (will be gzipped)
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
field	the genotypes to convert should come from the "GT" or "DS" fields
verbose	verbosity level (0/1)

Value

an invisible list with both output file paths

Author(s)

Timothee Flutre

See Also

gtVcf2dose, dsVcf2dose, filterVariantCalls

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