text: user6380: 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 values 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 home_alt etc
  Any simple explanation for beginner like me (with no background in bioinformatics/biology) can be helpful
  
  user3694: 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.
  
  user6251: 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 <tab> C,CA <tab> 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?
  
original_text: 6380: <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 values 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 home_alt etc</p>
  <p>Any simple explanation for beginner like me (with no background in bioinformatics/biology) can be helpful</p>
   3694: <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>
   6251: <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>
  <p><a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" rel="nofollow noreferrer">VCF - Variant Call Format</a><br />
  <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><br />
  <a href="https://www.biostars.org/p/377242/" rel="nofollow noreferrer">Difference between 0/0 and ./. for genotype in VCF</a><br />
  <a href="https://www.biostars.org/p/187068/" rel="nofollow noreferrer">1/2 in VCF genotype field?</a></p>
  