exportVCF: Generates a VCF file from phased haplotypes

In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

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.

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on April 7, 2024, 7:13 p.m.