Manipulate Variant Call Format (Vcf) files. — VcfFile • VariantAnnotation

Use VcfFile() to create a reference to a Vcf file (and its index). Once opened, the reference remains open across calls to methods, avoiding costly index re-loading.

VcfFileList() provides a convenient way of managing a list of VcfFile instances.

usage

## Constructors

VcfFile: VcfFile(file, index = paste(file, "tbi", sep="."), ..., yieldSize=NA_integer_)
VcfFileList: VcfFileList(..., yieldSize=NA_integer_)

## Accessors

index: index(object)
path: path(object, ...)
isOpen: isOpen(con, rw="")
yieldSize: yieldSize(object, ...)
yieldSize<-: yieldSize(object, ...) <- value
show: show(object)

## Opening / closing

open: open(con, ...)
close: close(con, ...)

## method

vcfFields: vcfFields(object)

arguments

con: An instance of VcfFile.
file: A character(1) vector to the Vcf file path; can be remote (http://, ftp://).
index: A character(1) vector of the Vcf file index (.tbi file).
yieldSize: Number of records to yield each time the file is read from using scanVcf or readVcf.
...: Additional arguments. For VcfFileList, this can either be a single character vector of paths to Vcf files, or several instances of VcfFile objects.
rw: character() indicating mode of file.

Objects from the Class

Objects are created by calls of the form VcfFile().

Fields

VcfFile and VcfFileList classes inherit fields from the TabixFile and TabixFileList classes.

Functions and methods

VcfFile and VcfFileList classes inherit methods from the TabixFile and TabixFileList classes.

## Opening / closing:

open: Opens the (local or remote) path and index. Returns a VcfFile instance. yieldSize determines the number of records parsed during each call to scanVcf or readVcf; NA indicates that all records are to be parsed.
close: Closes the VcfFile con; returning (invisibly) the updated VcfFile. The instance may be re-opened with open.VcfFile.

## Accessors:

path: Returns a character(1) vector of the Vcf path name.
index: Returns a character(1) vector of Vcf index (tabix file) name.
yieldSize, yieldSize<-: Return or set an integer(1) vector indicating yield size.

## Methods:

vcfFields: Returns a CharacterList of all available VCF fields, with names of fixed, info, geno and samples indicating the four categories. Each element is a character() vector of available VCF field names within each category. It works for both local and remote vcf file.

Author

Valerie Obenchain

Examples

fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation",
                  mustWork=TRUE)
vcffile <- VcfFile(fl)
vcffile
#> class: VcfFile 
#> path: /private/var/folders/yw/gfhgh7k565v9w83x_k764wbc0000gp/.../chr7-sub.vcf.gz
#> index: /private/var/folders/yw/gfhgh7k565v9w83x_k764wbc00.../chr7-sub.vcf.gz.tbi
#> isOpen: FALSE 
#> yieldSize: NA 
vcfFields(fl)
#> CharacterList of length 4
#> [["fixed"]] REF ALT QUAL FILTER
#> [["info"]] CGA_BF CGA_BNDG CGA_BNDGO CGA_FI CGA_MEDEL ... MATEID NS SS SVTYPE
#> [["geno"]] GT AD CGA_BNDDEF CGA_BNDMPC CGA_BNDP CGA_BNDPOS ... DP FT GQ HQ PS
#> [["samples"]] HCC1187-H-200-37-ASM-N1 HCC1187-H-200-37-ASM-T1
vcfFields(vcffile)
#> CharacterList of length 4
#> [["fixed"]] REF ALT QUAL FILTER
#> [["info"]] CGA_BF CGA_BNDG CGA_BNDGO CGA_FI CGA_MEDEL ... MATEID NS SS SVTYPE
#> [["geno"]] GT AD CGA_BNDDEF CGA_BNDMPC CGA_BNDP CGA_BNDPOS ... DP FT GQ HQ PS
#> [["samples"]] HCC1187-H-200-37-ASM-N1 HCC1187-H-200-37-ASM-T1

param <- GRanges("7", IRanges(c(55000000,  55900000), width=10000))
vcf <- readVcf(vcffile, "hg19", param=param)
dim(vcf)
#> [1] 45  2

## `vcfFields` also works for remote vcf filepath.  
if (FALSE) { # \dontrun{
chr22url <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
vcfFields(chr22url)
} # }