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VQL language

sacha schutz edited this page Oct 24, 2019 · 28 revisions

Select statement

SELECT chr,pos FROM variants 
SELECT chr,pos FROM variants WHERE pos > 30 
SELECT chr,pos, gene FROM variants WHERE gene = 'CFTR'
SELECT chr,pos, gene FROM variants WHERE gene in ('CFTR','GJB2')
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE gene in ('CFTR','GJB2') AND transcripts = "truc"
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE sample("boby").GT = 1
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE sample("boby").isHetero = True
SELECT chr,pos, gene, sample("boby").GT, HOMO_COUNT FROM variants
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE consequence has "exon"
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE regulation has "iron_transport"
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE gene in set("hpo")
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE gene in set("hpo")
SELECT chr,pos, gene, sample("boby").GT FROM variants WHERE case_count = 3 and normal_count = 0

### Create Statement

CREATE boby FROM variants WHERE gene in set("hpo")
CREATE boby FROM variants IN BED("exome.bed")
CREATE truc = variant - boby
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