Hello!

I am trying to apply snpgdsLDpruning to data from the UK Biobank but am running into an error saying, "The GDS node "genotype/data" does not exist." I have converted the downloaded bgen files to gds and tried the code below.

Code:

library(SeqArray)
library(SAIGEgds)
library(SNPRelate)

# gds_fn is the path to our chromosome 22 gds file.
gds <- seqOpen(gds_fn)

set.seed(1000)
snpset <- snpgdsLDpruning(gds)

Output:

Loading required package: gdsfmt
Loading required package: Rcpp
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
SNV pruning based on LD:
Calculating allele counts/frequencies ...
Error in seqApply(f, "genotype", margin = "by.variant", as.is = "list",  :
  The GDS node "genotype/data" does not exist.
Calls: snpgdsLDpruning ... eval -> <Anonymous> -> seqParallel -> FUN -> seqApply
Execution halted

I am new to the GDS file type, so any help and insight would be greatly appreciated. Thanks!

Alyssa