The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?