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Old 10-04-2015, 02:53 PM   #4
Len Trigg
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Location: New Zealand

Join Date: Jun 2011
Posts: 29

While this post is a little old, it is worth noting that the joint Bayesian variant calling of RTG Core does directly incorporate pedigree information during the primary variant calling, right where it can have the most effect.

Pedigree post-processors (such as FamSeq, Polymutt, DeNovoGear) are probably fine for SNPs, but for more complex variants (where the hypothesis space is much larger) the caller has already made a pedigree-oblivious decision as to which potential alleles to output GLs for.
Len Trigg, Ph.D.
Real Time Genomics
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