I usually do one quality control step at a time, so i can see the resulting plink file and save removed snps (--bfile org.plink --remove new.plink --out removed.snps). I wonder if it can be done if one step somehow?
Please provide a more detailed description of what you want, including at least one .log file from a command you actually ran. The example command line you provided is too garbled, with at least one flag that’s outright wrong.
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