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Difference between Genotype 0|1 and 1|0 in VCF file?

I have a VCF file, I tried to find the total number of each GT. The result came out :

COUNT-----GT 
   4789----- 0/1 
  13621---- 0|1
  10701----- 1|0
  20462----- 1|1

I know 0 is for Ref. allele and 1 for first ALT allele, but why some are represented as 0|1 and some as 1|0 ?

gt calling genotype vcf variant
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updated by Jeremy Leipzig Jeremy Leipzig • written by ved_vyas • ved_vyas

1 answer

The order of alleles matters only when the variants are phased,

for unphased heterozygous mutations, there is no difference between 0/1 and 1/0, by convention it is written as 0/1

when we have phased variants then the order matters, 0|1 and 1|0 are used to indicate which variants are in the same phase.

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written by Istvan Albert Istvan Albert

we should note a typical phasing algorithm can't follow a "mom|dad" convention, for instance, because they have no knowledge of the trio pedigree. You just know that 1|0 is from one parent and 0|1 is from the other with respect to other variants.

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written by Jeremy Leipzig Jeremy Leipzig

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