varanno

Source code

Description

Annotate genetic variants with VCF databases.

Usage

varanno(
  chr = NULL,
  start = NULL,
  end = NULL,
  ref = NULL,
  alt = NULL,
  strand = NULL,
  vcf = NULL,
  tags = NULL,
  check.alt.only = FALSE
)

Arguments

chr Vector of chromosome names.
start Vector of start positions.
end Vector of end positions.
ref Vector of reference alleles.
alt Vector of alternative alleles.
strand Vector of strands.
vcf VCF database. Should be indexed with ‘bcftools index’ at first.
tags Vector of tags to annotate. Require VCF database specified, and tags should be well formated in the VCF header.
check.alt.only Only annotate records for alternative allele (non-ref allele). Default is FASLE.
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