annotateQ: Run VariantAnnotation on the provided variants

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

Run VariantAnnotation on the provided variants

Description

Run VariantAnnotation on the provided variants

Usage

annotateQ(
  q,
  genome = "hg19",
  resourceDirectory = "superFreqResources",
  reference,
  cpus = 1
)

Arguments

q	data.frame: The variants to be annotated.
genome	character: hg19, hg38 or mm10.
reference	character: Path to the reference fasta.
cpus	integer: The number of cpus to be used as most.
annotationDirectory	character: Where the annotation resources are taken from.

Details

This function calls VEP on the output from outputSomaticVariants. For this, VEP needs to be callable by system('vep').

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.