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> | ||
− | + | nref_i = 0.5 * depth_i * (1 + {(lss_i - lrr_i)\over lss_i + lrr_i - 2 * lrs_i + 6 * depth_i}) \ | |
</math> | </math> | ||
:<math> | :<math> | ||
− | AB = | + | AB = {0.05 + \sum_i P_i(het) * nref_i\over 0.10 + \sum_i P_i(het)*depth_i} |
</math> | </math> | ||
+ | |||
+ | == Points == | ||
+ | |||
+ | Three points for correctly deciphering why this formula works. |
Latest revision as of 15:22, 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.