<p>0 and 1 is just a way of coding the reference (0) and alternate (1) allele. These could be A/G, C/T etc. It's just a simplified way of expressing the different alleles.</p>
<p><code>0/1</code> and <code>1/0</code> functionally mean the same thing (that the individual is a heterozygote) - since the genotype is unphased, the alleles aren't ordered. The <code>/</code> symbol tells you the genotype is unphased. However, in practice, a heterozygous genotype is always written as <code>0/1</code> as a matter of convention. <code>0/0</code> is referred to as homozygous reference, and <code>1/1</code> as homozygous alternative.</p>
<p><code>0|1</code> and <code>1|0</code> <strong>do</strong> mean something different, since the pipe symbol <code>|</code> tell us the order of the alleles matters.</p>
<p>Occasionally you will have multi allelic positions, where you have more than one alternate allele, and therefore the field will look like:</p>
<pre><code>Ref   Alt
A   [C,GT]
</code></pre>
<p>The extra alt allele is given the number 2, so in this case if an individual had the genotype CT then their genotype code would be 0/2.</p>
<p>Full detail is given in the official <a href="https://samtools.github.io/hts-specs/VCFv4.2.pdf" rel="noreferrer">VCF specification page.</a></p>

CC BY-SA 4.0
2020-09-14T10:23:10.190Z
2020-09-14T11:35:11.667Z
2020-09-14T11:35:11.667Z
user438383
<p>You can get most of the info from this <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218" rel="nofollow noreferrer">paper</a>. See Fig. 1 and the surrounding text. Quoting from there, &quot;GT, genotype, encodes alleles as numbers: 0 for the reference allele, 1 for the first allele listed in ALT column, 2 for the second allele listed in ALT and so on.&quot;</p>
<p>In your case, the reference allele, here a single nucleotide, is A. When the alternate allele is also A, the genotype GT is reference, or 0. There are 2 copies of each allele in the human genome in non-sex chromosomes chr1-chr22, hence 0/0, or homozygous reference or HOM_REF.</p>
<p>When ALT=G, and the GT column is 0/1, this means that you have 1 reference allele (0), and 1 alternate allele (1). This means that you have A on one copy of this locus, and G on another. The convention is write GT field in ascending order, so 0/1 rather than 1/0. This is called heterozygous, or HET.</p>
<p>When ALT=C,CA, the GT is probably 1/2, because there are 2 alternate alleles, and I assume we continue with the same chromosome present in 2 copies. This means there are no reference alleles here at all, only alternate alleles. It is a heterozygous genotype composed of two different ALT alleles, or HET_ALT. Note that it is not enclosed in square brackets in the vcf file format: <code>A &lt;tab&gt; C,CA &lt;tab&gt; 1/2 ...</code>.</p>
<p>Finally, these are some examples of HOM_ALT:</p>
<pre><code>A    C     1/1
A    G     1/1
A    CA    1/1
</code></pre>
<p>This means that the same ALT allele (either C, or G, or CA) is present in 2 copies. There is no reference allele present. This is called homozygous alternate genotype.</p>
<p>In general, the name <em>homo</em> means the same, and <em>hetero</em> means different, in the context of genotypes.</p>
<p><strong>REFERENCES:</strong></p>
<p>Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-2158. doi:10.1093/bioinformatics/btr330 : <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/</a></p>
<p><strong>SEE ALSO:</strong></p>
<ul>
<li><a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" rel="nofollow noreferrer">VCF - Variant Call Format</a></li>
<li><a href="https://www.biostars.org/p/86321/" rel="nofollow noreferrer">What Does Genotype (&quot;0/0&quot;, &quot;0/1&quot; Or &quot;1/1&quot;) In *.Vcf File Represent?</a></li>
<li><a href="https://www.biostars.org/p/377242/" rel="nofollow noreferrer">Difference between 0/0 and ./. for genotype in VCF</a></li>
<li><a href="https://www.biostars.org/p/187068/" rel="nofollow noreferrer">1/2 in VCF genotype field?</a></li>
</ul>

CC BY-SA 4.0
2020-09-14T12:13:07.950Z
2023-04-04T16:08:47.913Z
2023-04-04T16:08:47.913Z
Timur Shtatland
<p>As <a href="https://stackoverflow.com/q/63851080/680068">my question in SO</a> was closed and asked to be posted in this forum, I am posting it here.</p>
<p>I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain basics related to the GT field in the VCF file.</p>
<p>I know we have a field called <code>Alleles</code>. May I know under what circumstances GT takes a certain value and how they are called? Can you confirm my understanding?</p>
<pre><code>Ref Alt    GT   Name 
A    A     0/0  Homozygous
A    G     0/1  Heterozygous (does 1/0 also mean the same?) What's this 0 and 1 actually?
A   [C,CA] ??    ??
??   ??    1/1  HOM_ALT? How and why? 
</code></pre>
<p>Can the experts here help me to fill the <code>question marks</code> and also help me understand with the Ref and Alt combinations when a genotype can take a value of 0/0 or 1/0 or 1/1 or 1/2 etc. and what are the names for those values? Like when it is called HOM_ALT etc.?</p>
<p>Any simple explanation for beginner like me (with no background in bioinformatics/biology) can be helpful.</p>

<vcf><file-formats>
How is the GT field in a VCF file defined?
# How is the GT field in a VCF file defined?

(Asked by: username_0 on 2020-09-14)

As my question in SO was closed and asked to be posted in this forum, I am posting it here.
I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain basics related to the GT field in the VCF file.
I know we have a field called Alleles. May I know under what circumstances GT takes a certain value and how they are called? Can you confirm my understanding?
Ref Alt    GT   Name 
A    A     0/0  Homozygous
A    G     0/1  Heterozygous (does 1/0 also mean the same?) What's this 0 and 1 actually?
A   [C,CA] ??    ??
??   ??    1/1  HOM_ALT? How and why? 

Can the experts here help me to fill the question marks and also help me understand with the Ref and Alt combinations when a genotype can take a value of 0/0 or 1/0 or 1/1 or 1/2 etc. and what are the names for those values? Like when it is called HOM_ALT etc.?
Any simple explanation for beginner like me (with no background in bioinformatics/biology) can be helpful.

**Tags:** vcf, file-formats

---

## 2 answers

### Answer by username_2 on 2020-09-14. Score: 7 | Accepted answer

You can get most of the info from this paper. See Fig. 1 and the surrounding text. Quoting from there, "GT, genotype, encodes alleles as numbers: 0 for the reference allele, 1 for the first allele listed in ALT column, 2 for the second allele listed in ALT and so on."
In your case, the reference allele, here a single nucleotide, is A. When the alternate allele is also A, the genotype GT is reference, or 0. There are 2 copies of each allele in the human genome in non-sex chromosomes chr1-chr22, hence 0/0, or homozygous reference or HOM_REF.
When ALT=G, and the GT column is 0/1, this means that you have 1 reference allele (0), and 1 alternate allele (1). This means that you have A on one copy of this locus, and G on another. The convention is write GT field in ascending order, so 0/1 rather than 1/0. This is called heterozygous, or HET.
When ALT=C,CA, the GT is probably 1/2, because there are 2 alternate alleles, and I assume we continue with the same chromosome present in 2 copies. This means there are no reference alleles here at all, only alternate alleles. It is a heterozygous genotype composed of two different ALT alleles, or HET_ALT. Note that it is not enclosed in square brackets in the vcf file format: A  C,CA  1/2 ....
Finally, these are some examples of HOM_ALT:
A    C     1/1
A    G     1/1
A    CA    1/1

This means that the same ALT allele (either C, or G, or CA) is present in 2 copies. There is no reference allele present. This is called homozygous alternate genotype.
In general, the name homo means the same, and hetero means different, in the context of genotypes.
REFERENCES:
Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-2158. doi:10.1093/bioinformatics/btr330 : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/
SEE ALSO:

VCF - Variant Call Format
What Does Genotype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent?
Difference between 0/0 and ./. for genotype in VCF
1/2 in VCF genotype field?


---

### Answer by username_1 on 2020-09-14. Score: 7

0 and 1 is just a way of coding the reference (0) and alternate (1) allele. These could be A/G, C/T etc. It's just a simplified way of expressing the different alleles.
0/1 and 1/0 functionally mean the same thing (that the individual is a heterozygote) - since the genotype is unphased, the alleles aren't ordered. The / symbol tells you the genotype is unphased. However, in practice, a heterozygous genotype is always written as 0/1 as a matter of convention. 0/0 is referred to as homozygous reference, and 1/1 as homozygous alternative.
0|1 and 1|0 do mean something different, since the pipe symbol | tell us the order of the alleles matters.
Occasionally you will have multi allelic positions, where you have more than one alternate allele, and therefore the field will look like:
Ref   Alt
A   [C,GT]

The extra alt allele is given the number 2, so in this case if an individual had the genotype CT then their genotype code would be 0/2.
Full detail is given in the official VCF specification page.


---

