Difference between revisions of "Genotype Likelihood Based Allele Balance"

Latest revision as of 15:22, 22 October 2010

A statistic developed by Dr. Tom Blackwell.

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}}

Three points for correctly deciphering why this formula works.

@@ Line 7: / Line 7: @@
 ; lsr : phred-scaled likelihood of observed bases given heterozygous genotype
 ; lss : phred-scaled likelihood of observed bases given non-reference genotype
+== Calculation ==
 :<math>
-nref = {0.5 * depth * (1 + (lss - lrr)\over(lss + lrr - 2 * lrs + 6 * depth))} \
+nref_i = 0.5 * depth_i * (1 + {(lss_i - lrr_i)\over lss_i + lrr_i - 2 * lrs_i + 6 * depth_i}) \
 </math>
 :<math>
-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_i\over 0.10 + \sum_i P_i(het)*depth_i}
 </math>
+== Points ==
+Three points for correctly deciphering why this formula works.