format_vcf: format_vcf
In mcanouil/rain: Reference-based Ancestry INference

format_vcf

R Documentation

format_vcf

format_vcf

format_vcf(
  input_vcfs,
  ref1kg_vcfs,
  ref1kg_maf,
  ichr,
  quality_tag,
  quality_threshold,
  output_directory,
  recode,
  bin_path
)

`input_vcfs`	A `character`. A path to one or several VCFs file.
`ref1kg_vcfs`	A `character`. A path to the reference VCFs files (i.e., 1,000 Genomes sequencing data).
`ref1kg_maf`	A `numeric`. MAF threshold for SNPs in 1,000 Genomes
`ichr`	A `character` or `numeric`. The chromosome identifier.
`quality_tag`	A `character`. Name of the imputation quality tag for `"array"`, e.g., `"INFO"` or `"R2"`. Default is `NULL`.
`quality_threshold`	A `numeric`. The threshold to keep/discard SNPs based on their imputation quality.
`output_directory`	A `character`. The path where the data and figures is written.
`recode`	A `character`. Which VCF should be filtered and recode, either `"all"` or `"input"`.
`bin_path`	A `list(character)`. A list giving the binary path of `vcftools`, `bcftools`, `bgzip`, `tabix` and `plink`.