https://github.com/corearray/gds2bgen
R package for the format conversion from bgen to gds
https://github.com/corearray/gds2bgen
bgen gds
Last synced: about 1 month ago
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R package for the format conversion from bgen to gds
- Host: GitHub
- URL: https://github.com/corearray/gds2bgen
- Owner: CoreArray
- Created: 2018-11-20T02:36:13.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-03-03T21:01:28.000Z (3 months ago)
- Last Synced: 2025-03-30T11:23:36.998Z (2 months ago)
- Topics: bgen, gds
- Language: C++
- Homepage:
- Size: 39.8 MB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
Awesome Lists containing this project
README
gds2bgen: Format Conversion from BGEN to GDS
===
[GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html)
## Description
This package provides functions for format conversion from [bgen](http://bgenformat.org) files to [SeqArray GDS](https://github.com/zhengxwen/SeqArray) files.
* gds2bgen has been moved to https://github.com/CoreArray/gds2bgen from https://github.com/zhengxwen/gds2bgen since Feb 2025.
## Version
v0.9.4
## Package Maintainer
Dr. Xiuwen Zheng ([[email protected]]([email protected]))
## Installation
Requires R (≥ v3.5.0), [gdsfmt](http://www.bioconductor.org/packages/gdsfmt) (≥ v1.20.0), [SeqArray](http://www.bioconductor.org/packages/SeqArray) (≥ v1.24.0)
* Installation from Github:
```R
library("devtools")
install_github("CoreArray/gds2bgen")
```
The `install_github()` approach requires that you build from source, i.e. `make` and compilers must be installed on your system -- see the [R FAQ](http://cran.r-project.org/faqs.html) for your operating system; you may also need to install dependencies manually.
Or manually intall the package
```sh
git clone https://github.com/CoreArray/gds2bgen
cd gds2bgen/src
unzip bgen_v1.1.8.zip
cd bgen_v1.1.8
python ./waf configure
python ./waf
cp build/libbgen.a ..
cp build/3rd_party/zstd-1.1.0/libzstd.a ..
rm -rf build
sleep 1; touch ../libbgen.a
cd ../../..
R CMD INSTALL gds2bgen
```
## Copyright Notice
This package includes the sources of the bgen library (https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk), Boost (the C++
libraries, https://www.boost.org) and Zstandard (https://zstd.net).
## Citations for GDS
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. *Bioinformatics*. [DOI: 10.1093/bioinformatics/bts606](http://dx.doi.org/10.1093/bioinformatics/bts606).
Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance data format for WGS variant calls. *Bioinformatics*. [DOI: 10.1093/bioinformatics/btx145](http://dx.doi.org/10.1093/bioinformatics/btx145).
## Examples
```R
library(gds2bgen)
seqBGEN_Info() # bgen library version
## "bgen_lib_v1.1.8"
bgen_fn <- system.file("extdata", "example.8bits.bgen", package="gds2bgen")
# or bgen_fn <- "your_bgen_file.bgen"
seqBGEN_Info(bgen_fn)
## File: gds2bgen/extdata/example.8bits.bgen
## # of samples: 500
## # of variants: 199
## Compression method: zlib
## Layout version: v1.2
## Unphased: TRUE
## # of bits: 8
## Ploidy: 2
## sample id: sample_001, sample_002, sample_003, sample_004, ...
# example.8bits.bgen ==> example.gds, using 4 cores
seqBGEN2GDS(bgen_fn, "example.gds",
storage.option="LZMA_RA", # compression option, e.g., ZIP_RA for zlib or LZ4_RA for LZ4
float.type="packed8", # 8-bit packed real numbers
geno=FALSE, # 2-bit integer genotypes, stored in 'genotype/data'
dosage=TRUE, # numeric alternative allele dosages, stored in 'annotation/format/DS'
prob=FALSE, # numeric genotype probabilities, stored in 'annotation/format/GP'
parallel=4 # the number of cores
)
# show file structure
library(SeqArray)
(f <- seqOpen("example.gds"))
seqClose(f)
## File: example.gds (137.7K)
## + [ ] *
## |--+ 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 [ ] *
## |--+ phase [ ]
## |--+ annotation [ ]
## | |--+ id { Str8 199 LZMA_ra(18.6%), 321B } *
## | |--+ qual { Float32 199 LZMA_ra(11.8%), 101B } *
## | |--+ filter { Int32 199 LZMA_ra(11.3%), 97B } *
## | |--+ info [ ]
## | \--+ format [ ]
## | |--+ DS [ ] *
## | | \--+ data { PackedReal8U 500x199 LZMA_ra(55.6%), 54.0K } *
## \--+ sample.annotation [ ]
```
## Also See
[seqVCF2GDS()](https://rdrr.io/bioc/SeqArray/man/seqVCF2GDS.html) in the [SeqArray](https://bioconductor.org/packages/SeqArray) package, conversion from VCF files to GDS files.
[seqBED2GDS()](https://rdrr.io/bioc/SeqArray/man/seqBED2GDS.html) in the [SeqArray](https://bioconductor.org/packages/SeqArray) package, conversion from PLINK BED files to GDS files.