Add BGEN to GDS conversion

README.md

@@ -4,7 +4,9 @@ This is a tutorial for (1) automatically functionally annotating the variants of
 **FAVORannotator**, **STAARpipeline** and **STAARpipelineSummary** are implemented as a collection of apps. Please see the apps <a href="https://github.com/xihaoli/favorannotator-rap">**favorannotator**</a>, <a href="https://github.com/xihaoli/staarpipeline-rap">**staarpipeline**</a>, <a href="https://github.com/xihaoli/staarpipelinesummary_varset-rap">**staarpipelinesummary_varset**</a> and <a href="https://github.com/xihaoli/staarpipelinesummary_indvar-rap">**staarpipelinesummary_indvar**</a> that run on the UK Biobank Research Analysis Platform for more details.
 ## Pre-step of association analysis using STAARpipeline 
 ### Generate Genomic Data Structure (GDS) file
-R/Bioconductor package **SeqArray** provides functions to convert the genotype data (in VCF/BCF/PLINK BED/SNPRelate format) to SeqArray GDS format. For more details on usage, please see the R/Bioconductor package <a href="https://bioconductor.org/packages/release/bioc/html/SeqArray.html">**SeqArray**</a> [<a href="https://bioconductor.org/packages/release/bioc/manuals/SeqArray/man/SeqArray.pdf">manual</a>]. A wrapper for the seqVCF2GDS function in the SeqArray package can be found <a href="convertVCF2GDS.R">**here**</a> (**Credit: Michael R. Brown and Jennifer A. Brody**).
+R/Bioconductor package **SeqArray** provides functions to convert the genotype data (in VCF/BCF/PLINK BED/SNPRelate format) to SeqArray GDS format. For more details on usage, please see the R/Bioconductor package <a href="https://bioconductor.org/packages/release/bioc/html/SeqArray.html">**SeqArray**</a> [<a href="https://bioconductor.org/packages/release/bioc/manuals/SeqArray/man/SeqArray.pdf">manual</a>]. A wrapper for the `seqVCF2GDS`/`seqBCF2GDS` function in the SeqArray package can be found <a href="convertVCF2GDS.R">**here**</a> (**Credit: Michael R. Brown and Jennifer A. Brody**).
+
+R package **gds2bgen** provides functions to convert the genotype data (in BGEN format) to SeqArray GDS format. For more details on usage, please see the R package <a href="https://github.com/zhengxwen/gds2bgen">**gds2bgen**</a>. An example for the `seqBGEN2GDS` function in the gds2bgen package can be found <a href="https://github.com/zhengxwen/gds2bgen#examples">**here**</a> (**Credit: Xiuwen Zheng**).
 
 Note: After the GDS file is generated, there is supposed to be a channel in the GDS file (default is `annotation/filter`) where all variants passing the quality control (QC) should be labeled as `"PASS"`. If there is no such channel for a given post-QC GDS file (where all variants in the GDS file are pass variants), one can create a new channel in the GDS file by setting the value of all variants as `"PASS"`. An example script can be found <a href="Add_QC_label.R">**here**</a>. Then, in all scripts of STAARpipeline, `QC_label <- "annotation/filter"` should be updated to `QC_label <- "annotation/info/QC_label"`.