Calculate LD matrix from bgen file

formatting error: Calculate LD matrix from bgen file


I am new to plink and am learning as I go.

I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below:

./plink2/plink2 --r2 bin --bgen ukb_imp_chr1_v3_qc2.bgen --ld-snp-list rsids --ld-window-r2 0.8 --out samplesnp_ld

PLINK v2.00a3LM 64-bit Intel (4 Aug 2021)
(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to samplesnp_ld.log.
Options in effect:
  --bgen ukb_imp_chr1_v3_qc2.bgen
  --ld-snp-list rsids
  --ld-window-r2 0.8
  --out samplesnp_ld
  --r2 bin

Start time: Sat Aug  7 15:40:36 2021
Error: --bgen now requires a REF/ALT mode ('ref-first', 'ref-last', or
'ref-unknown').  As of this writing, raw UK Biobank files are ref-first, while
older and PLINK-exported BGEN files are more likely to be ref-last.
For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

Hence I am wondering if anyone might know how to deal with this problem. I have not found any posts where this was an error. I have only seen this being a warning see: plink2 bgen to vcf ukbiobank

Hence is it possible to flip the variants and create a copy bgen file for this to work. Or is this file format irreconcilable with the latest version of plink2





Source link