writeVcf {VariantAnnotation} | R Documentation

## Write VCF files

### Description

Write Variant Call Format (VCF) files to disk

### Usage

    ## S4 method for signature 'VCF,character'
    writeVcf(obj, filename, index = FALSE, ...)
    ## S4 method for signature 'VCF,connection'
    writeVcf(obj, filename, index = FALSE, ...)

### Arguments

`obj` | Object containing data to be written out. At present only accepts VCF.
`filename` | The character() name of the VCF file, or a connection (e.g., `file()`), to be written out. A connection opened with `open = "a"` will have header information written only if the file does not already exist.
`index` | Whether to bgzip the output file and generate a tabix index.
`...` | Additional arguments, passed to methods. nchunk: Integer or NA. When provided this argument overrides the default chunking behavior of `writeVcf`, see Details section. An integer value specifies the number of records in each chunk; NA disables chunking.

### Details

A VCF file can be written out from data in a `VCF` object. More general methods to write out from other objects may be added in the future.

`writeVcf` writes out the header fields in a `VCF` object 'as-is' with the exception of these key-value pairs:

- fileformat: When missing, a line is added at the top of the file with the current supported version. `VariantAnnotation` >=1.27.6 supports VCFv4.3.

- fileDate: When missing, a line is added with today's date. If the key-value pair exists, the date is overwritten with today's date.

- contig: When missing, `VariantAnnotation` attempts to use the `Seqinfo` of the `VCF` object to determine the contig information.

Large VCF files (i.e., > 1e5 records) are written out in chunks; VCF files with < 1e5 records are not chunked. The optimal number of records per chunk depends on both the number of records and complexity of the data. Currently `writeVcf` determines records per chunk based on the total number of records only. To override this behavior or experiment with other values use `nchunk` as an integer or NA. An integer value represents the number of records per chunk regardless of the size of the VCF; NA disables all chunking.

- writeVcf(vcf, tempfile()) ## default chunking

- writeVcf(vcf, tempfile(), nchunk = 1e6) ## chunk by 1e6

- writeVcf(vcf, tempfile(), nchunk = NA) ## no chunking

### Value

VCF file

### Note

NOTE: `VariantAnnotation` >= 1.27.6 supports VCFv4.3. See the NOTE on the `?VCFHeader` man page under the `meta()` extractor for a description of how header parsing has changed to accommodate the new header lines with key name of 'META'.

### Author(s)

Valerie Obenchain and Michael Lawrence

### 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

`readVcf`

### Examples

      fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")

      out1.vcf <- tempfile()
      out2.vcf <- tempfile()
      in1 <- readVcf(fl, "hg19")
      writeVcf(in1, out1.vcf)
      in2 <- readVcf(out1.vcf, "hg19")
      writeVcf(in2, out2.vcf)
      in3 <- readVcf(out2.vcf, "hg19")
      stopifnot(all(in2 == in3))

      ## write incrementally
      out3.vcf <- tempfile()
      con <- file(out3.vcf, open="a")
      writeVcf(in1[1:2,], con)
      writeVcf(in1[-(1:2),], con)
      close(con)
      readVcf(out3.vcf, "hg19")

[Package VariantAnnotation version 1.28.13 Index]