Answers.Body: <p>This is easy to check, you can download both specs in .tex format and do <code>diff</code>.</p>
  
  <p>Changes to the v4.2 compared to v4.1:</p>
  
  <ol>
  <li>Information field format: adding source and version as recommended fields.</li>
  <li>INFO field can have one value for each possible allele (code <code>R</code>).</li>
  <li>For all of the ##INFO, ##FORMAT, ##FILTER, and ##ALT metainformation, extra fields can be included after the default fields.</li>
  <li>Alternate base (ALT) can include <code>*</code>: missing due to a upstream deletion.</li>
  <li>Quality scores, a sentence removed: <em>High QUAL scores indicate high confidence calls. Although traditionally people use integer phred scores, this field is permitted to be a floating point to enable higher resolution for low confidence calls if desired.</em></li>
  <li>Examples changed a bit.</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-24T10:44:27.877Z
Answers.Text: Doing a raw diff against the spec files seems pretty silly, ideally theres documented differences somewhere, but thanks for summarizing this!
Answers.UserDisplayName: Colin D
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-24T10:47:53.927Z
Answers.Text: Would also be worth generating a comparison with 4.3
Answers.UserDisplayName: Colin D
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-01T11:40:33.550Z
Answers.LastActivityDate: 2017-06-01T11:40:33.550Z
Answers.UserDisplayName: Iakov Davydov
Body: <p>What are the key differences between VCF versions 4.1 and 4.2?
   It looks like v4.3 contains a changelog (specs available <a href="http://samtools.github.io/hts-specs/" rel="noreferrer">here</a>) but earlier specifications do not. </p>
  
  <p><a href="https://www.biostars.org/p/211152/" rel="noreferrer">This</a> biostar post points out one difference: the introduction of <code>Number=R</code> for fields with one value per allele including REF — can anyone enumerate the other changes between these two versions?</p>
  
Tags: <vcf><htslib><file-formats>
Title: What's the difference between VCF spec versions 4.1 and 4.2?
ThreadText: # What's the difference between VCF spec versions 4.1 and 4.2?
  
  (Asked by: username_0 on 2017-06-01)
  
  What are the key differences between VCF versions 4.1 and 4.2?
  It looks like v4.3 contains a changelog (specs available [here](http://samtools.github.io/hts-specs/)) but earlier specifications do not.
  
  [This](https://www.biostars.org/p/211152/) biostar post points out one difference: the introduction of `Number=R` for fields with one value per allele including REF — can anyone enumerate the other changes between these two versions?
  
  **Tags:** vcf, htslib, file-formats
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-06-01. Score: 16 | Accepted answer
  
  This is easy to check, you can download both specs in .tex format and do `diff`.
  
  Changes to the v4.2 compared to v4.1:
  
  1. Information field format: adding source and version as recommended fields.
  2. INFO field can have one value for each possible allele (code `R`).
  3. For all of the ##INFO, ##FORMAT, ##FILTER, and ##ALT metainformation, extra fields can be included after the default fields.
  4. Alternate base (ALT) can include `*`: missing due to a upstream deletion.
  5. Quality scores, a sentence removed: *High QUAL scores indicate high confidence calls. Although traditionally people use integer phred scores, this field is permitted to be a floating point to enable higher resolution for low confidence calls if desired.*
  6. Examples changed a bit.
  
  > **Comments:**
  > **username_2**: Doing a raw diff against the spec files seems pretty silly, ideally theres documented differences somewhere, but thanks for summarizing this!  
  > **username_2**: Would also be worth generating a comparison with 4.3  
  
  ---
  
  