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ABHom Annotation Formula

Posts: 30Member
edited October 2012

Hello,

For the “ABHom” annotations, the VCF header gives the following formula : (A/(A+O)). What does the 'O' stand for?

Thanks,
Mika

Post edited by Geraldine_VdAuwera on
Tagged:

• Posts: 511Member, GATK Dev, DSDE Dev mod

They're the same metric, the samples that they are calculated on are stratified by the genotype call. So A and O represent reference and alternate. Or maybe alternate and other

Geraldine Van der Auwera, PhD

• Posts: 30Member

Hi Geraldine,

Thank you for your reply. I am familiar with the definition in the link you have posted. However, I am not able to find a page/link that elaborates further on the ABHom annotation.

~Mika

Well, the formula is just a short notation for "fraction of ref bases over ref + alt bases", so the "O" simply stands for alt bases. We don't have any more detailed documentation than that, what else would you like to know?

Geraldine Van der Auwera, PhD

• Posts: 30Member

Okay, this definition seems to tally with what is given for ABHet in the VCF header.

ABHet,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))"

I am still unclear about what the terms A and O represent in the formula below:

ABHom,Number=1,Type=Float,Description="Allele Balance for homs (A/(A+O))"

Thanks,
Mika

• Posts: 511Member, GATK Dev, DSDE Dev mod

They're the same metric, the samples that they are calculated on are stratified by the genotype call. So A and O represent reference and alternate. Or maybe alternate and other