seqGDS2VCF {SeqArray} | R Documentation |
Converts a SeqArray GDS file to a Variant Call Format (VCF) file.
seqGDS2VCF(gdsfile, vcf.fn, info.var=NULL, fmt.var=NULL, use_Rsamtools=TRUE, verbose=TRUE)
gdsfile |
a |
vcf.fn |
the file name, output a file of VCF format; or a
|
info.var |
a list of variable names in the INFO field, or NULL for
using all variables; |
fmt.var |
a list of variable names in the FORMAT field, or NULL for
using all variables; |
use_Rsamtools |
TRUE for loading the Rsamtools package, see details |
verbose |
if |
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.
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.
# 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)