<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>

CC BY-SA 4.0
2018-07-24T10:44:27.877Z
Doing a raw diff against the spec files seems pretty silly, ideally theres documented differences somewhere, but thanks for summarizing this!
Colin D
CC BY-SA 4.0
2018-07-24T10:47:53.927Z
Would also be worth generating a comparison with 4.3
Colin D
CC BY-SA 3.0
2017-06-01T11:40:33.550Z
2017-06-01T11:40:33.550Z
Iakov Davydov
<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>

<vcf><htslib><file-formats>
What's the difference between VCF spec versions 4.1 and 4.2?
# 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

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## 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  

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