Genotype phased and unphased

Question

[manjumoorthy95]

Can anybody tell help me explain the difference between 0/1 and 0|1 genotype when, we do snp analysis. I read that it shows the difference in phasing of the genotype, with 0/1 not phased and 0|1 phased. But what does it mean to be phased and unphased?

Answer 1

[Pierre Lindenbaum]

the variants are known to be on the same homologous chromosome because some reads were found to carry both variants.

so 0|1 means the genotypes is phased with the previous or/and next variant.

[manjumoorthy95]

So does that mean 0|1, means that the allele is changed to a new one, while 0/1 means, the allele is not changed?

[Pierre Lindenbaum]

no, in both cases it's a heterozygous genotype, but he second is phased with another variant

[manjumoorthy95]

OK, Thank you so much

[manjumoorthy95]

What does, 0/0 mean? Does that mean the reference allele has not changed?

[manjumoorthy95]

Can you explain to me what is meant by 0/0, 1/1, 0|0 and 1|1? Iam totally confused.

[Pierre Lindenbaum]

https://samtools.github.io/hts-specs/VCFv4.2.pdf "1.4.2: genotype fields"

[Pierre Lindenbaum]

Does that mean the reference allele has not changed?

YES. 0/0 = diploid, both alleles match the reference genome.

[manjumoorthy95]

if both the alleles match the reference genome, then why is it reported as a snp?