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What does a genotype "*/*" mean?

After calling SNPs, I get the genotype from the result such as "A/A", "./.", "/". So whate does "/" mean? Is it different from "./."? Hope for your help.

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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Lyc

    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).

    VCF v4.3 specification reserves the * allele to reference overlapping deletions. This is not to be confused with the bracketed asterisk <*> used to denote symbolic alternate alleles.

    I hope this helps.

    Regards
    Bhanu

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