text: user131: I went through the manuals and can't find the meaning of the below flag:
  -filt_rules_l 'filter==0'
  
  Here is the link to manual for this flag: filt_rules_l
  Can anyone explain?
  IMPUTE version: 
  impute_v2.3.1_x86_64_dynamic
  
  
  Edit: The full IMPUTE2 code is irrelevant, I am not using the command to impute, I received an imputed data and the script used to impute. This one flag was a mystery to me. I will update the post with impute software version when I find out.
  
  user939: I have never used this program, but reading the manual in the link it has to mean the following.
  The manual says:
  
  Writing -filt_rules_l 'eur.maf<0.05' on the command line would tell the program to remove any variants with eur.maf values less than 0.05 from the reference panel.
  
  So, -filt_rules_l 'filter==0' would mean that the program removes any variants with filter values of 0 from the reference panel. In the legend file there should be a column named filter, which are filtered out when the value is 0.
  Here is the example legend file, in your case there must be a custom additional column named "filter":
  $ head ALL_1000G_phase1integrated_v3_chr1_impute.legend
  
  id position a0 a1 afr.aaf amr.aaf asn.aaf eur.aaf afr.maf amr.maf asn.maf eur.maf
  rs58108140 10583 G A 0.0407 0.1713 0.1311 0.2071 0.0407 0.1713 0.1311 0.2071
  rs189107123 10611 C G 0.0142 0.0276 0.0140 0.0211 0.0142 0.0276 0.0140 0.0211
  
  
original_text: 131: <p>I went through the manuals and can't find the meaning of the below flag:</p>
  
  <pre><code>-filt_rules_l 'filter==0'
  </code></pre>
  
  <p>Here is the link to manual for this flag: <a href="https://mathgen.stats.ox.ac.uk/impute/filtering_options.html" rel="nofollow noreferrer">filt_rules_l</a></p>
  
  <p>Can anyone explain?</p>
  
  <p>IMPUTE version: </p>
  
  <pre><code>impute_v2.3.1_x86_64_dynamic
  </code></pre>
  
  <hr>
  
  <p><strong>Edit:</strong> The full IMPUTE2 code is irrelevant, I am <strong>not</strong> using the command to impute, I received an imputed data and the script used to impute. This one flag was a mystery to me. I will update the post with impute software version when I find out.</p>
   939: <p>I have never used this program, but reading the manual in the link it has to mean the following.</p>
  
  <p>The manual says:</p>
  
  <blockquote>
    <p>Writing <code>-filt_rules_l 'eur.maf&lt;0.05'</code> on the command line would tell the program to remove any variants with <code>eur.maf</code> values less than 0.05 from the reference panel.</p>
  </blockquote>
  
  <p>So, <code>-filt_rules_l 'filter==0'</code> would mean that the program removes any variants with <code>filter</code> values of 0 from the reference panel. In the legend file there should be a column named <code>filter</code>, which are filtered out when the value is 0.</p>
  
  <p>Here is the example legend file, in your case there must be a custom additional column named <em>"filter"</em>:</p>
  
  <pre><code>$ head ALL_1000G_phase1integrated_v3_chr1_impute.legend
  
  id position a0 a1 afr.aaf amr.aaf asn.aaf eur.aaf afr.maf amr.maf asn.maf eur.maf
  rs58108140 10583 G A 0.0407 0.1713 0.1311 0.2071 0.0407 0.1713 0.1311 0.2071
  rs189107123 10611 C G 0.0142 0.0276 0.0140 0.0211 0.0142 0.0276 0.0140 0.0211
  </code></pre>
  