Question: Genotype phased and unphased
0
gravatar for manjumoorthy95
18 months ago by
manjumoorthy9520 wrote:

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?

snp genotype phasing vcf • 1.1k views
ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum131k • written 18 months ago by manjumoorthy9520
2
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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.

ADD COMMENTlink written 18 months ago by Pierre Lindenbaum131k

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?

ADD REPLYlink written 18 months ago by manjumoorthy9520

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

ADD REPLYlink written 18 months ago by Pierre Lindenbaum131k

OK, Thank you so much

ADD REPLYlink written 18 months ago by manjumoorthy9520

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

ADD REPLYlink written 18 months ago by manjumoorthy9520

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

ADD REPLYlink written 18 months ago by manjumoorthy9520

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

ADD REPLYlink written 18 months ago by Pierre Lindenbaum131k

Does that mean the reference allele has not changed?

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

ADD REPLYlink written 18 months ago by Pierre Lindenbaum131k

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

ADD REPLYlink written 18 months ago by manjumoorthy9520
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