[New plugin] Check variant for miss-validation

[antonylebechec]

A plugin to check miss-validated variants:

• "Variants already validated in some samples but not all of them"

SELECT distinct(variant_id) FROM sample_has_variant WHERE sample_has_variant.classification IN (2) AND sample_has_variant.gt >=1 GROUP BY sample_has_variant.classification, sample_has_variant.variant_id INTERSECT SELECT variant_id FROM sample_has_variant WHERE sample_has_variant.classification IN (0) AND sample_has_variant.gt >=1 GROUP BY sample_has_variant.classification, sample_has_variant.variant_id

• "Variants not validated but classified as Pathogenic (ACMG-5)"

SELECT distinct(variant_id) FROM sample_has_variant WHERE sample_has_variant.classification IN (0) AND sample_has_variant.gt >=1 AND sample_has_variant.variant_id IN (SELECT id FROM variants WHERE variants.classification IN (5))

• "Variants not validated but classified as Pathogenic (ACMG-5) or Likely pathogenic (ACMG-4)"

SELECT distinct(variant_id) FROM sample_has_variant WHERE sample_has_variant.classification IN (0) AND sample_has_variant.gt >=1 AND sample_has_variant.variant_id IN (SELECT id FROM variants WHERE variants.classification IN (4,5))