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={0.5*depth*(1+(lss-lrr) \over (lss+lrr-2*lrs+6*depth))}\$

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

Points

Three points for correctly deciphering why this formula works.