annotateSomaticQs: Run VariantAnnotation on the provided samples

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

Run VariantAnnotation on the provided samples

Description

Run VariantAnnotation on the provided samples

Usage

annotateSomaticQs(
  qs,
  genome = "hg19",
  resourceDirectory = "superFreqResources",
  reference,
  cpus = 1
)

Arguments

qs	list of data.frame: The variants to be annotated by sample
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 uses the VariantAnnotation package to annotate somatic variants. PolyPHen, SIFT and exon number are removed when switching from VEP.

ChristofferFlensburg/superFreq documentation built on July 8, 2024, 7:51 a.m.