BcfInput {Rsamtools} | R Documentation

## Operations on ‘BCF’ files.

### Description

Import, coerce, or index variant call files in text or binary format.

### Usage

    scanBcfHeader(file, ...)
    ## S4 method for signature 'character'
    scanBcfHeader(file, ...)

    scanBcf(file, ...)
    ## S4 method for signature 'character'
    scanBcf(file, index = file, ..., param=ScanBcfParam())

    asBcf(file, dictionary, destination, ...,
          overwrite=FALSE, indexDestination=TRUE)
    ## S4 method for signature 'character'
    asBcf(file, dictionary, destination, ...,
          overwrite=FALSE, indexDestination=TRUE)

    indexBcf(file, ...)
    ## S4 method for signature 'character'
    indexBcf(file, ...)

### Arguments

`file` | For `scanBcf` and `scanBcfHeader`, the character() file name of the ‘BCF’ file to be processed, or an instance of class `BcfFile`.
`index` | The character() file name(s) of the ‘BCF’ index to be processed.
`dictionary` | a character vector of the unique “CHROM” names in the VCF file.
`destination` | The character(1) file name of the location where the BCF output file will be created. For `asBcf` this is without the “.bcf” file suffix.
`param` | A instance of `ScanBcfParam` influencing which records are parsed and the ‘INFO’ and ‘GENO’ information returned.
`...` | Additional arguments, e.g., for `scanBcfHeader,character-method`, `mode` of `BcfFile`.
`overwrite` | A logical(1) indicating whether the destination can be over-written if it already exists.
`indexDestination` | A logical(1) indicating whether the created destination file should also be indexed.

### Details

`bcf*` functions are restricted to the GENO fields supported by ‘bcftools’ (see documentation at the url below). The argument `param` allows portions of the file to be input, but requires that the file be BCF or bgzip'd and indexed as a `TabixFile`. For similar functions operating on VCF files see ?`scanVcf` in the `VariantAnnotation` package.

### Value

`scanBcfHeader` returns a list, with one element for each file named in `file`. Each element of the list is itself a list containing three elements. The `Reference` element is a character() vector with names of reference sequences. The `Sample` element is a character() vector of names of samples. The `Header` element is a DataFrameList with one DataFrame per unique key value in the header (preceded by “##”).

NOTE: In Rsamtools >=1.33.6, the `Header` DataFrameList no longer contains a DataFrame named "META". The META DataFrame contained all "simple" key-value headers lines from a bcf / vcf file. These "simple" header lines are now parsed into individual DataFrames named for the unique key.

`scanBcf` returns a list, with one element per file. Each list has 9 elements, corresponding to the columns of the VCF specification: `CHROM`, `POS`, `ID`, `REF`, `ALT` `QUAL`, `FILTER`, `INFO`, `FORMAT`, `GENO`.

The `GENO` element is itself a list, with elements corresponding to fields supported by ‘bcftools’ (see documentation at the url below).

`asBcf` creates a binary BCF file from a text VCF file.

`indexBcf` creates an index into the BCF file.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>.

### References

http://vcftools.sourceforge.net/specs.html outlines the VCF specification.

http://samtools.sourceforge.net/mpileup.shtml contains information on the portion of the specification implemented by `bcftools`.

http://samtools.sourceforge.net/ provides information on `samtools`.

### See Also

`BcfFile`, `TabixFile`

### Examples

    fl <- system.file("extdata", "ex1.bcf.gz", package="Rsamtools",
                      mustWork=TRUE)
    scanBcfHeader(fl)
    bcf <- scanBcf(fl)
    ## value: list-of-lists
    str(bcf[1:8])
    names(bcf[["GENO"]])
    str(head(bcf[["GENO"]][["PL"]]))
    example(BcfFile)

[Package Rsamtools version 2.0.3 Index]