seqGDS2VCF: Convert to a VCF File
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	seqGDS2VCF(gdsfile, vcf.fn, info.var=NULL, fmt.var=NULL, chr_prefix="", use_Rsamtools=TRUE, verbose=TRUE)

`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
`chr_prefix`	the prefix of chromosome, e.g., "chr"; no prefix by default
`use_Rsamtools`	`TRUE` for loading the Rsamtools package, see details
`verbose`	if `TRUE`, show information

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 and use_Rsamtools=TRUE, the exported file utilizes the bgzf format (bgzip, a variant of gzip format) allowing for fast indexing.

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

Xiuwen Zheng

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.

seqVCF2GDS

# 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)