apt-probeset-genotype is a program for making genotype calls from Affymetrix SNP microarrays. It currently implements three different genotype calling algorithms: BRLMM (pronounced ”B-realm”) - a model based approach similar to the RLMM (pronounced ”realm”) model developed by Nusrat Rabbee and Terry Speed but with a Bayesian extension, hence the ”B”. Currently requires seed genotypes for every SNP and sample analyzed which it obtains via the DM algorithm, hence it requires the presence of MisMatch (MM) probes. ...

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