importSomaticVariantsVEP: Import VEP-annotated VCF files obtained from HMF...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Imports the VCF obtained from HMF and further annotated by VEP. The annotation should have been performed using the workflow available at: https://github.com/J0bbie/VariantAnnotation_VEP

Usage

importSomaticVariantsVEP(
  pathVCF,
  passOnly = TRUE,
  gnomADe = 0.001,
  gnomADg = 0.005,
  keepAnnotation = TRUE
)

Arguments

pathVCF	(character): Path to the <CPCT>_post_processed.vcf file containing Strelka2 somatic variants.
passOnly	(logical): Only import variant which passed all Strelka2 and PON filters. This also filters variants based on PON filter (>5 PON occurences).
gnomADe	(double): Maximum allele frequency in the gnomADe database.
gnomADg	(double): Maximum allele frequency in the gnomADg database.
keepAnnotation	(logical): Import and interpret the ANN column?

Value

(VRanges) VRanges object containing the somatic variants and assorted annotations.

Author(s)

Job van Riet [e-mail]

See Also

Other CPCT: detectKataegis_OLD(), findCPCTCenter(), importLINXFusions(), importPurityStatsPURPLE(), importSomaticCopynumberPURPLE(), importStructuralVariantsPURPLE(), importWGSOfCohort(), importWGSOfSample(), importdriverCatalogHMF(), performCHORD(), performShatterSeek()

Examples

	# Path to VEP annotated VCF.
	path <- '<CPCT#R>_<CPCT#T>_post_processed.hg19_multianno.vcf'

	sampleX.somaticVariants <- importCPCT.somaticVariants(path, passOnly = TRUE)

	# View variant annotation.
	do.call(rbind, sampleX.somaticVariants$annotation)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.