Allele Balance for ABHets & ABHom

mikawinmikawin Member
edited October 2012 in Ask the GATK team

Hello,
Is there a threshold value for the annotation ‘Allele Balance’ to call the SNP as heterozygous or homozygous call? I have calls where ABHet=0.073 and ABHom=0.100; it would have been more appropriate to call the former an alternate homozygous call and the latter as homozygous with the reference and not called at all by UG.

Thanks,
Mika

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    Hi Mika,

    We don't recommend use of the Allele Balance annotation (which is why it's not part of the Standard package of annotations). You should feel free to use it for whatever specific analysis you'd like, but you certainly cannot draw any conclusions from the ABHet or ABHom values to the genotype calls in UG.

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    Hi Mika,

    We don't recommend use of the Allele Balance annotation (which is why it's not part of the Standard package of annotations). You should feel free to use it for whatever specific analysis you'd like, but you certainly cannot draw any conclusions from the ABHet or ABHom values to the genotype calls in UG.

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