text: user61: What are the key differences between VCF versions 4.1 and 4.2?
   It looks like v4.3 contains a changelog (specs available here) but earlier specifications do not. 
  This 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?
  
  user191: 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:
  
  Information field format: adding source and version as recommended fields.
  INFO field can have one value for each possible allele (code R).
  For all of the ##INFO, ##FORMAT, ##FILTER, and ##ALT metainformation, extra fields can be included after the default fields.
  Alternate base (ALT) can include *: missing due to a upstream deletion.
  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.
  Examples changed a bit.
  
  
original_text: 61: <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>
   191: <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>
  