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spent the week working on the J2EE application bomcat. See sources.
Query from SLS
predictions SIFT/PPH2 for each individuals:
select S.name,F.prediction,P.prediction,count(distinct V.id) from (sample as S,vcf_call as C,variation as V) left join sift as F on F.variation_id=V.id left join polyphen as P on P.variation_id=V.id where C.sample_id=S.id and C.input_id >=3 and C.input_id<=22 and C.variation_id=V.id and F.prediction is not null and P.prediction is not null group by S.id,F.prediction,P.prediction;