Question

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

1

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2.5 years ago

ved_vyas ▴ 10

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 • 3.2k views

ADD COMMENT • link updated 2.5 years ago by Jeremy Leipzig 22k • written 2.5 years ago by ved_vyas ▴ 10

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What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent?

ADD REPLY • link 2.5 years ago by zx8754 11k

score 2 · Answer 1 · 2021-10-12

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2.5 years ago

Istvan Albert 100k

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.

ADD COMMENT • link 2.5 years ago by Istvan Albert 100k

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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.

ADD REPLY • link 2.5 years ago by Jeremy Leipzig 22k