Error during target quality control

[Jalil Sharif]

I am trying to run the following code

```

plink2 /path/to/file/ukb_imp_chr1 --fam /rds/general/user/js4120/home/fam_files/ukb_imp_chr.fam --extract /path/to/file/ukb_imp_chr1.QC.snplist --indep-pairwise 200 50 0.25 --out /path/to/file/ukb_imp_chr1.QC

```

I then ran:
```
plink2 /path/to/file/ukb_imp_chr1 --fam /rds/general/user/js4120/home/fam_files/ukb_imp_chr.fam --extract /path/to/file/ukb_imp_chr1.QC.snplist --set-all-var-ids @:# --new-id-max-allele-len 1000 --rm-dup retain-mismatch  --indep-pairwise 200 50 0.25 --out /path/to/file/ukb_imp_chr1.QC
```

In both instances I am getting the following error:

```
Error: --indep-pairwise requires unique variant IDs. (--set-all-var-ids and/or
--rm-dup may help.)
```

[Christopher Chang]

Why are you using the retain-mismatch mode of --rm-dup?