<p>Hello all</p>

<p>I want remove some snp from map and also genotype from ped file. I used this command in plink:</p>

<pre><code>plink --file FILE  --exclude SNP-LIST-FILE
</code></pre>

<p>I think the some SNP in map file should be deleted and also genotype in ped, but when I check the number of raw in map and the column of ped file its same as before exclude</p>

<p>is there any one know my snp in snplist excluded or not? </p>

<p>thanks</p>

Your command is correct, but you should add two options: `--out` and `--recode`. If you don't specify these, plink executes the commands and prints a summary to the screen (and to the .log file), but does not actually write the results to a ped file nor overwrites your original data.

The `--recode` option specifies that you want to write a .ped file as output. The `--out` option specifies the suffix of the output file:

    plink --file mydata --exclude snp_list --recode --out filter_data

Also, check that the the SNP-LIST-FILE is formatted correctly. It must contain the ids of the SNPs that you want to remove.