text: user194: I'm using the Ensembl Variant Effect Predictor (VEP) to annotate VCF files, and I am trying to add some additional fields to the output, among these is OVERLAP_BP, which is listed here in available fields:
  
  OVERLAP_BP - Number of base pairs overlapping with the corresponding variation feature
  
  It's clear that some (many? all?) of these additional fields are only enabled by adding extra options to the VEP command (as listed on the RHS of the options table).
  For example, the ZYG field is made available by adding the --individual flag to the VEP call. 
  But OVERLAP_BP doesn’t appear in the output fields column on that page, and when I add it to the output using --fields, it is consistently empty.
  What options are required to make the OVERLAP_BP output field available to me in VEP?
  
  user194: I also opened this as a Github issue, and received the following response:
  
  It seems there are some inconsistencies on our end. I'm looking into it.
    Until the fix, using --fields OverlapBP,OverlapPC works with any output format, while --fields OVERLAP_BP,OVERLAP_PC works only with default output format.
  A small note that this overlap data is available for structural variants only.
  
  
original_text: 194: <p>I'm using the Ensembl Variant Effect Predictor (VEP) to annotate VCF files, and I am trying to add some additional fields to the output, among these is <code>OVERLAP_BP</code>, which is listed <a href="http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output" rel="nofollow noreferrer">here</a> in available fields:</p>
  
  <blockquote>
    <p>OVERLAP_BP - Number of base pairs overlapping with the corresponding variation feature</p>
  </blockquote>
  
  <p>It's clear that some (many? all?) of these additional fields are only enabled by adding extra options to the VEP command (as listed on the RHS of the <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" rel="nofollow noreferrer">options table</a>).</p>
  
  <p>For example, the <code>ZYG</code> field is made available by adding the <code>--individual</code> flag to the VEP call. </p>
  
  <p>But <code>OVERLAP_BP</code> doesn’t appear in the output fields column on that page, and when I add it to the output using <code>--fields</code>, it is consistently empty.</p>
  
  <p>What options are required to make the <code>OVERLAP_BP</code> output field available to me in VEP?</p>
   194: <p>I also opened this as a <a href="https://github.com/Ensembl/ensembl-vep/issues/204" rel="nofollow noreferrer">Github issue</a>, and received the following response:</p>
  
  <blockquote>
    <p>It seems there are some inconsistencies on our end. I'm looking into it.
    Until the fix, using <code>--fields OverlapBP,OverlapPC</code> works with any output format, while <code>--fields OVERLAP_BP,OVERLAP_PC</code> works only with default output format.</p>
    
    <p>A small note that this overlap data is available for structural variants only.</p>
  </blockquote>
  