After much reading I'm still confused about the interpretation of the SugDup output column in Annovar. It seems to derive from the genomic SuperDups track at UCSC. Is this track derived from Eichler's work? Does a variant with a SegDup score mean that it is definitely in a nonfunctional pseudogene? What are the dangers of dismissing variants with SegDup scores greater than 0.9 ? Any practical advice for a hunter of Mendelian Diseases of humans?
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Segmental duplication regions in the genome are hard to map to because the reads that match in that region can have multiple matches in other regions of the genome, so the variants need to be treated with caution.
Also I've heard people who do the molecular validation work on SNPs or Indels tell us that its not possible to validate anything in those regions so even if you discover something with reasonable confidence, you won't be able to design experiments to verify it.
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