Difference between revisions of "Genotype Likelihood Based Allele Balance"
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:<math> | :<math> | ||
− | nref = 0.5 * depth * {1 + (lss - lrr)\over | + | nref = 0.5 * depth * {1 + (lss - lrr)\over lss + lrr - 2 * lrs + 6 * depth} \ |
</math> | </math> | ||
:<math> | :<math> | ||
− | AB = | + | AB = {0.05 + \sum_i P_i(het) * nref\over 0.10 + \sum_i P_i(het)*depth} |
</math> | </math> | ||
Revision as of 15:19, 22 October 2010
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
Points
Three points for correctly deciphering why this formula works.