readVCF: Filtering the patient variants in VCF format annotated by VEP

In aschluter/ClinPrior: Disease Gene prioritization

Filtering the patient variants in VCF format annotated by VEP

Description

Filtering the patient variants in VCF format annotated by VEP

Usage

readVCF(
  sampleName,
  filter = "",
  geneQuality = 20,
  readDepth = 10,
  variants,
  assembly = "assembly37",
  distSplicThreshold = 1000,
  synonymous = TRUE
)

Arguments

sampleName	character name with the patient code as is written in the VCF file.
filter	character name with the desired filter to select the variants. It should be as is written in the FILTER column in the vcf file.
geneQuality	numeric value indicating the desired GQ threshold. Default 20.
readDepth	numeric value indicating the desired DP threshold. Default 10.
variants	object of class vcfR-class with the patient variants using the read.vcfR function from vcfR package.
assembly	Genome assembly used. Default assembly human GRCh37.
distSplicThreshold	integer indicating the maximum distance in base pairs (bp) allowed between intronic variants and the intron-exon boundary. Default 1000.
synonymous	logical indicating whether to include the synonymous variants. Default TRUE.

Value

returns an object of class vcfR-class.

Examples

library(vcfR)
vcfFile = paste(system.file("extdata/example", package = "ClinPrior"),"HG001_GRCh37_1_22_v4.2.1_benchmark.vep01.KCNQ2Met546Thr.vcf.gz",sep="/")
variants <- read.vcfR(vcfFile)
variantsFiltered <- readVCF(sampleName = "HG001",variants=variants)

aschluter/ClinPrior documentation built on Sept. 27, 2024, 3:46 a.m.