seqGDS2VCF {SeqArray} | R Documentation

## Convert to a VCF File

### Description

Converts a SeqArray GDS file to a Variant Call Format (VCF) file.

### Usage

    seqGDS2VCF(gdsfile, vcf.fn, info.var=NULL, fmt.var=NULL, use_Rsamtools=TRUE,
        verbose=TRUE)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object
`vcf.fn` | the file name, output a file of VCF format; or a `connection` object
`info.var` | a list of variable names in the INFO field, or NULL for using all variables; `character(0)` for no variable in the INFO field
`fmt.var` | a list of variable names in the FORMAT field, or NULL for using all variables; `character(0)` for no variable in the FORMAT field
`use_Rsamtools` | `TRUE` for loading the Rsamtools package, see details
`verbose` | if `TRUE`, show information

### Details

`seqSetFilter` can be used to define a subset of data for the export.

If the filename extension is "gz", the gzip compression algorithm is used to compress the output data. When the Rsamtools package is installed, the exported file utilizes the bgzf format (bgzip, a variant of gzip format) allowing for fast indexing.

### Value

Return the file name of VCF file with an absolute path.

### Author(s)

Xiuwen Zheng

### References

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

### See Also

`seqVCF2GDS`

### Examples

    # the GDS file
    (gds.fn <- seqExampleFileName("gds"))

    # display
    (f <- seqOpen(gds.fn))

    # output the first 10 samples
    samp.id <- seqGetData(f, "sample.id")
    seqSetFilter(f, sample.id=samp.id[1:5])

    # convert
    seqGDS2VCF(f, "tmp.vcf.gz")

    # no INFO and FORMAT
    seqGDS2VCF(f, "tmp1.vcf.gz", info.var=character(), fmt.var=character())

    # output BN,GP,AA,DP,HM2 in INFO (the variables are in this order), no FORMAT
    seqGDS2VCF(f, "tmp2.vcf.gz", info.var=c("BN","GP","AA","DP","HM2"),
        fmt.var=character())

    # read
    (txt <- readLines("tmp.vcf.gz", n=20))
    (txt <- readLines("tmp1.vcf.gz", n=20))
    (txt <- readLines("tmp2.vcf.gz", n=20))

    #########################################################################
    # Users could compare the new VCF file with the original VCF file
    # call "diff" in Unix (a command line tool comparing files line by line)

    # using all samples and variants
    seqResetFilter(f)

    # convert
    seqGDS2VCF(f, "tmp.vcf.gz")

    # file.copy(seqExampleFileName("vcf"), "old.vcf.gz", overwrite=TRUE)
    # system("diff <(gunzip -c old.vcf.gz) <(gunzip -c tmp.vcf.gz)")

    # 1a2,3
    # > ##fileDate=20130309
    # > ##source=SeqArray_RPackage_v1.0

    # LOOK GOOD!

    # delete temporary files
    unlink(c("tmp.vcf.gz", "tmp1.vcf.gz", "tmp2.vcf.gz"))

    # close the GDS file
    seqClose(f)

[Package SeqArray version 1.28.1 Index]