setGt2Na: Set GT to NA

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

Set GT to NA

Description

Set genotypes (GT field) to missing if the genotype quality (GQ field) isn't high enough.

Usage

setGt2Na(
  vcf.file,
  genome = "",
  out.file,
  yieldSize = NA_integer_,
  dict.file = NULL,
  seq.id = NULL,
  seq.start = NULL,
  seq.end = NULL,
  min.gq = 90,
  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")
out.file	path to the output VCF file (a bgzip index will be created in the same directory)
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	sequence identifier to work on (e.g. "chr2")
seq.start	start of the sequence to work on (if NULL, whole seq)
seq.end	end of the sequence to work on (if NULL, whole seq)
min.gq	minimum GQ below which GT is set to missing
verbose	verbosity level (0/1)

Value

the destination file path as an invisible character(1)

Author(s)

Timothee Flutre

See Also

filterVariantCalls

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