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Trio or SelectVariants

I have 25 samples of exome sequencing data from 6 families on normal and diseased individuals. Two are joint families with data available for affected/unaffected uncles and aunts. I am not sure if I should run trio for this or SelectVariants (normal vs diseased) (or if there is another, more appropriate way).

If I run trio, then I have only about 10 complete trios. The uncles and aunts are part of incomplete trios and I am not sure if those samples will be of much use in calling disease specific mutations. If I run SelectVariants, I will be able to include all samples but I think trio analysis will be more accurate.

The third possibility is performing the analysis in both ways and then selecting the common variants. The hypothesis is that the common variants will be high-confidence variants.

Any ideas?


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