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

format_sequencing

R Documentation

format_sequencing

format_sequencing

format_sequencing(
  cohort_name,
  input_vcfs,
  output_directory,
  ref1kg_vcfs,
  ref1kg_maf,
  recode,
  vcf_half_call,
  bin_path
)

`cohort_name`	A `character`. A name to describe the studied population compared to 1,000 Genomes.
`input_vcfs`	A `character`. A path to one or several VCFs file.
`output_directory`	A `character`. The path where the data and figures is written.
`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
`recode`	A `character`. Which VCF should be filtered and recode, either `"all"` or `"input"`.
`vcf_half_call`	A `character`. The mode to handle half-call. + 'haploid'/'h': Treat half-calls as haploid/homozygous (the PLINK 1 file format does not distinguish between the two). This maximizes similarity between the VCF and BCF2 parsers. + 'missing'/'m': Treat half-calls as missing (default). + 'reference'/'r': Treat the missing part as reference.
`bin_path`	A `list(character)`. A list giving the binary path of `vcftools`, `bcftools`, `bgzip`, `tabix` and `plink`.