1. Return all information from the variant table

SELECT * from variant

2. Return all variants with MAF > 0.1

SELECT * from variant v
WHERE v.maf > 0.1

3. For each sample, find all genes and variants where the given sample has either:

1. a single, homozygous, LOF mutation and that sample is the _only_ sample with that mutation.
2. two or more heterozygous LOF mutations (i.e., a possible compound heterozygote), and that sample is the _only_ sample with those mutations.

::

SELECT v.*, gt.genotype, g.gene FROM variant v,

genotype gt, sample s, gene ge

WHERE v.variant_id = gt.variant_id

AND gt.sample_id = s.sample_id AND v.gene_id = ge.gene_id AND s.sample = “NA00001” AND v.lof = 1 AND (v.num_het = 1 OR v.num_hom_alt = 1) AND g.genotype != “hom_ref” AND g.genotype != “unknown”

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