Closed CreRecombinase closed 3 years ago
It appears that while it is possible to obtain dosage information from bgen files using dosage=TRUE, using geno=TRUE doesn't work:
bgen
dosage=TRUE
geno=TRUE
> bgen_fn <- system.file("extdata", "example.8bits.bgen", package="gds2bgen") > seqBGEN2GDS(bgen_fn,"example.gds",geno=TRUE,dosage=FALSE,prob=FALSE,parallel=4) ... > si <- seqOpen("example.gds") > si Object of class "SeqVarGDSClass" File: /scratch/t.cri.nknoblauch/intersect_snplist/example.gds (6.8K) + [ ] * |--+ description [ ] * |--+ sample.id { Str8 500 LZMA_ra(7.02%), 393B } * |--+ variant.id { Int32 199 LZMA_ra(33.9%), 277B } * |--+ position { Int32 199 LZMA_ra(60.6%), 489B } * |--+ chromosome { Str8 199 LZMA_ra(15.7%), 101B } * |--+ allele { Str8 199 LZMA_ra(11.8%), 101B } * |--+ genotype [ ] * | |--+ data { Bit2 2x500x0 LZMA_ra, 18B } * | |--+ extra.index { Int32 3x0 LZMA_ra, 18B } * | \--+ extra { Int16 0 LZMA_ra, 18B } |--+ phase [ ] | |--+ data { Bit1 500x0 LZMA_ra, 18B } * | |--+ extra.index { Int32 3x0 LZMA_ra, 18B } * | \--+ extra { Bit1 0 LZMA_ra, 18B } |--+ annotation [ ]
Any thoughts as to what's happening here? Am i correct that without genotype information, I will be unable to export to plink/BED format?
genotype
It appears that while it is possible to obtain dosage information from
bgen
files usingdosage=TRUE
, usinggeno=TRUE
doesn't work:Any thoughts as to what's happening here? Am i correct that without
genotype
information, I will be unable to export to plink/BED format?