Genotype Likelihood Based Allele Balance

A statistic developed by Dr. Tom Blackwell.

Inputs

depth

at each site

lrr

phred-scaled likelihood of observed bases given reference genotype

lsr

phred-scaled likelihood of observed bases given heterozygous genotype

lss

phred-scaled likelihood of observed bases given non-reference genotype

Calculation

$nref_{i}=0.5*depth_{i}*(1+{(lss_{i}-lrr_{i}) \over lss_{i}+lrr_{i}-2*lrs_{i}+6*depth_{i}})\$

$AB={0.05+\sum _{i}P_{i}(het)*nref_{i} \over 0.10+\sum _{i}P_{i}(het)*depth_{i}}$

Points

Three points for correctly deciphering why this formula works.