polarise_ancestral_vcf: Polarise a VCF File setting the (supplied) Ancestral Allele...

In pygmyperch/melfuR: A collection of ugly R functions for analysis of SNP and spatial data.

Polarise a VCF File setting the (supplied) Ancestral Allele as REF

Description

This function reads a VCF file, reorders the REF and ALT alleles based on the ancestral allele specified in the INFO field (ID=AA) (the AA INFO field must be present in the vcf), adjusts the REF, ALT and genotype (GT) fields accordingly, and writes the modified VCF to a new file.

Usage

polarise_ancestral_vcf(
  input_vcf,
  output_vcf = "output.vcf.gz",
  compress = NULL
)

Arguments

input_vcf	Path to the input VCF file.
output_vcf	Path to the output VCF file. If not provided, defaults to "output.vcf.gz".
compress	Optional boolean indicating whether to compress the output file. If not provided, it will automatically detect based on the input file.

Value

The function writes the modified VCF file to the specified output path and returns a modified vcfR object to the environment

Examples

polarise_ancestral_vcf("input.vcf")

pygmyperch/melfuR documentation built on Aug. 26, 2024, 12:48 a.m.