Operations on ‘BCF’ files.
Import, coerce, or index variant call files in text or binary format.
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, ...)file |
For |
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 |
param |
A instance of |
... |
Additional arguments, e.g., for
|
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. |
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.
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, ALTQUAL, 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.
Martin Morgan <mtmorgan@fhcrc.org>.
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.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.