HaplotypeCaller what is j in calculation of genotype likelihood?
I have read the Methods and Algorithm section HC step 4: Assigning per-sample genotypes. I follow up until the equation for P(D|G) that includes a product over j. Please explain what j is. Are you taking half the likelihood of one read given allele 1 plus half the likelihood of that read given allele 2 and then taking the product of this over all reads?