View source: R/runVariantAnnotation.R
annotateSomaticQs | R Documentation |
Run VariantAnnotation on the provided samples
annotateSomaticQs(
qs,
genome = "hg19",
resourceDirectory = "superFreqResources",
reference,
cpus = 1
)
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. |
This function uses the VariantAnnotation package to annotate somatic variants. PolyPHen, SIFT and exon number are removed when switching from VEP.
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