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) www.cog-genomics.org/plink/2.0/ (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
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