Physical Phasing oh alleles

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Shanmugavadivel Subramaniam

• September 27, 2023 08:09

REQUIRED for all errors and issues:
a) GATK version used: 4
b) Exact command used:
c) Entire program log:

I could observe alleles at specified site as  0|1, 1|0 and 1|1 GT. are they hetero zygote as per physical phasing concept?.

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  Gökalp Çelik

  • September 27, 2023 08:17

  Hi Shanmugavadivel Subramaniam

  Numeric values in GT fields represent the allele present in the genotype. 0 represents REF alelle whereas 1 represents the first ALT allele, 2 represents the secont ALT allele and so on. If you have only a single number present at both sides of the phase or genotype sign then that site is homozygous. Otherwise different numbers mean heterozygosity if the sample is diploid. So in short 1|1 is HOM_ALT and 0|1 or 1|0 is HET. 

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