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We're interested in implementing Pasaniuc et al.'s (Nature Genetics 2012) method to use off-target next-generation sequencing data to 'genotype' some of our samples. In this paper, GATK’s UGCalcLikelihoods mode was used to compute the genotype likelihoods prior to imputation. Unfortunately, however, it doesn’t appear that UGCalcLikelihoods has been made available for public access. Is this true and can we anticipate that this might be available soon? Is there any way for members outside of Broad to access this?
If this is indeed unavailable this is a bit of a shame, both because this was published in such a high profile journal and, more importantly, because I'm certain that other researchers would like to use this method.
Can your suggest other tools that one might be able to use for this purpose?