I tried the following command to extract a bfile using a given snp list and a given subject ID list:

plink2 \
    --bgen xxx.bgen \
    --sample xxx.sample \
    --extract  input.snp_list \
    --make-bed \
    --out output

The input.snp_list is the second column from some other input.bim file. I hope to have alleles in the output.bim identical to the input.bim, but it's not case in the output.bim right now, because there are duplicate snps in the output.bim (like below),

19  rs75617501  0 44544721           T       C
19  rs75617501  0 44544721           T       G

and

19 rs573790568  0 44678292         TTG       T
19 rs573790568  0 44678292           T   TTGTG
19 rs573790568  0 44678292           T TTGTGTG

and rs75617501 and rs573790568 in the input.bim had no duplicates, and their corresponding alleles are

19 rs75617501  0 44544721  C  T

and

19 rs573790568  0 44678292 TTG  T

So I wonder if there is a way to remove the duplicated snps when extracting bfile so that only snps with alleles matching input.bim are kept. For example, after removing the duplicate snps I would only have the following in my output.bim:

19  rs75617501  0 44544721           T       C
19 rs573790568  0 44678292         TTG       T

Thank you!