Difference between revisions of "Genotype Likelihood Based Allele Balance"
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; lsr : phred-scaled likelihood of observed bases given heterozygous genotype | ; lsr : phred-scaled likelihood of observed bases given heterozygous genotype | ||
; lss : phred-scaled likelihood of observed bases given non-reference genotype | ; lss : phred-scaled likelihood of observed bases given non-reference genotype | ||
+ | |||
+ | == Calculation == | ||
:<math> | :<math> | ||
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AB = (0.05 + {\sum_i P_i(het) * nref)\over(0.10 + \sum_i P_i(het)*depth)} | AB = (0.05 + {\sum_i P_i(het) * nref)\over(0.10 + \sum_i P_i(het)*depth)} | ||
</math> | </math> | ||
+ | |||
+ | == Points == | ||
+ | |||
+ | Three points for correctly deciphering why this formula works. |
Revision as of 15:18, 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.