annoVAR

Source code

Description

Annotate genetic variants with preload GTF and/or VCF databases. Will generate gene region and other tags.

Usage

annoVAR(
  object = NULL,
  assay = NULL,
  gtf = NULL,
  vcf = NULL,
  tags = NULL,
  check.alt.only = FALSE,
  chr = "chr"
)

Arguments

object Seurat object.
assay Work assay.
gtf GTF object, load by gtf2db.
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. See VCF specification (https://samtools.github.io/hts-specs/VCFv4.2.pdf) for details.
check.alt.only Only annotate records for alternative allele (non-ref allele). Default is FASLE.
chr Colname name for chromsome, default is “chr”.

Value

Annotated Seurat object.

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