Genotype Likelihood Based Allele Balance

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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.