exportVCF: Generates a VCF file from phased haplotypes
In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

exportVCF

R Documentation

Generates a VCF file from phased haplotypes

Description

Generates a VCF file from phased haplotypes

Usage

exportVCF(
  index = NULL,
  outputfolder = NULL,
  phasedHap = NULL,
  positions = NULL,
  bsGenome = NULL,
  ref.fasta = NULL,
  chromosome = NULL,
  assume.biallelic = FALSE
)

Arguments

`index`	Unique identifier used to index analyzed individual/sample
`outputfolder`	Location to store created VCF file(s)
`phasedHap`	Data object containing phased haplotypes
`positions`	Set of heterozygous SNV positions used for phasing obtained from an input VCF files.
`bsGenome`	A `BSgenome` object which contains reference genome used to infer reference alleles.
`ref.fasta`	A user defined reference FASTA file to extract reference allele for all SNV positions.
`chromosome`	Name of the chromosome for which we want to export vcf file
`assume.biallelic`	If set to `TRUE` parameter 'snv.positions' is expected to contain biallelic loci (0/1, 1/0) and thus gaps in haplotypes will be filled accordingly.