Hi,
I'm wondering if it's possible to identify small contaminant populations using vireo and common variants? say, we have identified a major population of cells with the "correct" genotype and we want to find a (likely) small contaminating cell population with a different genotype among the remaining cells. I tried initializing vireoSNP.Vireo with n_donors=2, n_GT=2 and ID_prob_init=[.95,.05] for the "major" population and ID_prob_init=[.5,.5] for everything else. I'm assuming that after running vireo_object.fit(AD,DP) I should find the genotype assigment in np.argmax(vireo_object.ID_prob,axis=1). but the fit converges to an approximately even distribution of both genotypes, and the initial assignment is not respected (vireo_object.ID_prior is [.5,.5] for all cells after the fit).
do you think that's possible and I'm just not using vireo correctly? (otherwise a really great tool!)
thanks!
bobermayer
commented
3 years ago
Hi, I'm wondering if it's possible to identify small contaminant populations using vireo and common variants? say, we have identified a major population of cells with the "correct" genotype and we want to find a (likely) small contaminating cell population with a different genotype among the remaining cells. I tried initializing
vireoSNP.Vireowithn_donors=2,n_GT=2andID_prob_init=[.95,.05]for the "major" population andID_prob_init=[.5,.5]for everything else. I'm assuming that after runningvireo_object.fit(AD,DP)I should find the genotype assigment innp.argmax(vireo_object.ID_prob,axis=1). but the fit converges to an approximately even distribution of both genotypes, and the initial assignment is not respected (vireo_object.ID_prioris[.5,.5]for all cells after the fit). do you think that's possible and I'm just not usingvireocorrectly? (otherwise a really great tool!) thanks!