read.vcf: Read VCF
In jjellis/GenomicVis: Genomic Visualisation Routines

Description Usage Arguments Details Value Examples

Read a VCF file and return the called SNVs as a GRanges instance. Only SNVs with a single ALT allele are returned, and, by default, all filtered SNVs are excluded from the returned value.

1 2	read.vcf(f, genome, exclude.filtered = TRUE, read.info = FALSE, read.geno = FALSE, filter.func = NULL)

`f`	A `TabixFile` instance or character() name of the VCF file to be processed.
`genome`	A genome identifier.
`exclude.filtered`	filt
`read.info`	Read INFO field, default is to ignore the INFO field. Set this to `TRUE` if INFO fields are required in the filter function (see Details).
`read.geno`	Read genotypes from VCF, the default is to ignore the genotypes. Set this to `TRUE` if genotypes are needed in the filter function (see Details).
`filter.func`	a function used to filter variants from the returned `GRanges`

details

A VCF instance from the VariantAnnotation package.

## Not run: 
# To simply read a VCF excluding filtered variants use
x <- read.vcf(f, 'hg19', read.info = TRUE, filter.func = func)

# For more complicated filtering you can pass a filter function.  This
# example assuming the VCF has been annotated with SnpEff and we are only
# interested in variants that have not been filtered and have a SnpEff
# impact of HIGH or MODERATE.

func <- function(vcf) {
  x <- rowData(vcf)
  x[unlist(lapply(info(vcf)$EFF,
    function(x) any(grepl('(HIGH)|(MODERATE)', x))))]
}

f <- system.file('extdata', 'example.vcf', package = 'GenomicVis')
x <- read.vcf(f, 'hg19', read.info = TRUE, filter.func = func)

## End(Not run)