text: user2365: I have data in Plink format. I removed Indels using --snps-only command in Plink, but still some snps are as below:
  rs58119544;rs5746975    0   16915280    T   A
  
  I wonder, how i can get rid of these snps? the correct should be single snps without this (;) sign. Any idea to fix it please?
  
  user131: Use grep to get SNPs that have ";" in the name:
  >$ grep ";" myMap.txt | cut -f1 -d" " > myBadSNPs.txt
  
  Then use plink with --exclude :
  plink --file myFile
  --exclude myBadSNPs.txt
  --out myFileFiltered
  
  
original_text: 2365: <p>I have data in Plink format. I removed Indels using --snps-only command in Plink, but still some snps are as below:</p>
  
  <pre><code>rs58119544;rs5746975    0   16915280    T   A
  </code></pre>
  
  <p>I wonder, how i can get rid of these snps? the correct should be single snps without this (;) sign. Any idea to fix it please?</p>
   131: <p>Use <em>grep</em> to get SNPs that have <code>";"</code> in the name:</p>
  
  <pre><code>&gt;$ grep ";" myMap.txt | cut -f1 -d" " &gt; myBadSNPs.txt
  </code></pre>
  
  <p>Then use plink with <a href="https://www.cog-genomics.org/plink/1.9/filter#snp" rel="nofollow noreferrer">--exclude</a> :</p>
  
  <pre><code>plink --file myFile
  --exclude myBadSNPs.txt
  --out myFileFiltered
  </code></pre>
  