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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?

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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.
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  • $\begingroup$ Doing a raw diff against the spec files seems pretty silly, ideally theres documented differences somewhere, but thanks for summarizing this! $\endgroup$ – Colin D Jul 24 '18 at 10:44
  • $\begingroup$ Would also be worth generating a comparison with 4.3 $\endgroup$ – Colin D Jul 24 '18 at 10:47

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