simulRefseqCompatibleWithVcf: Fasta file

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

Fasta file

Description

Simulate a reference genome sequence compatible with alleles from genotype data in the VCF format. Useful with the GATK software.

Usage

simulRefseqCompatibleWithVcf(
  vcf.file = NULL,
  vcf.rng.all = NULL,
  chr.lengths = 10^5,
  fa.file = NULL,
  seed = NULL,
  verbose = 1
)

Arguments

vcf.file	path to the file in the VCF format (will be used only if vcf.rng.all=NULL
vcf.rng.all	data frame output from rngVcf2df
chr.lengths	vector of chromosome lengths (if a single number, will be repeated, i.e. all chromosomes will have the ame length)
fa.file	path to the output file in the fasta format (will be compressed via gzip if the name ends with gz); if NULL, the reference sequence will be returned as an object but not written into a file
seed	seed for the pseudo-random number generator (will be set only if non-NULL)
verbose	verbosity level (0/1)

Value

invisible DNAStringSet

Author(s)

Timothee Flutre

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