Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-15T14:59:38.343Z
Answers.LastActivityDate: 2018-05-15T14:59:38.343Z
Answers.UserDisplayName: sjcockell
Body: <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>
  
Tags: <vcf>
Title: How to add OVERLAP_BP field to VEP output?
ThreadText: # How to add OVERLAP_BP field to VEP output?
  
  (Asked by: username_0 on 2018-05-08)
  
  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](http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output) 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](http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html)).
  
  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?
  
  **Tags:** vcf
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-05-15. Score: 1 | Accepted answer
  
  I also opened this as a [Github issue](https://github.com/Ensembl/ensembl-vep/issues/204), 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.
  
  
  ---
  
  