ABHom Annotation Formula

mikawin

Hello,

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

Thanks, Mika

pdexheimer

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_VdAuwera

Please see this link: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_AlleleBalance.html

mikawin

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

Geraldine_VdAuwera

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?

mikawin

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

Geraldine_VdAuwera

What @pdexheimer said. It's ref and alt (not sure why they are called A and O).

pdexheimer

I checked the source - they are Allele and Other. This way the interpretation isn't dependent on whether the call is reference or not