# What's the difference between VCF spec versions 4.1 and 4.2?

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?

## 1 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.
• Doing a raw diff against the spec files seems pretty silly, ideally theres documented differences somewhere, but thanks for summarizing this! – Colin D Jul 24 '18 at 10:44
• Would also be worth generating a comparison with 4.3 – Colin D Jul 24 '18 at 10:47