What does below mean in GT field of VCF:
0/0
0/1
1/1
1/0
How are they related to REF and ALT fields and other fields?
Thanks, Ray
see my earlier answer A: VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased
GT genotype, encoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1 or 1|0 etc. For haploid calls, e.g. on Y, male X, mitochondrion, only one allele value should be given. All samples must have GT call information; if a call cannot be made for a sample at a given locus, ”.” must be specified for each missing allele in the GT field (for example ./. for a diploid). The meanings of the separators are:
/ : genotype unphased | : genotype phased
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Can you please explain little bit more?
can you please tell us what you don't understand.
0/0 - the sample is homozygous reference
0/1 - the sample is heterozygous, carrying 1 copy of each of the REF and ALT alleles
1/1 - the sample is homozygous alternate
What about 1/0?
1/0 is heterozygous too, it has the very same meaning than 0/1.
on the other hand
1|0 is not the same than 0|1 because genotypes are phased (the homologous chromosome is identified)