google-bigquerygoogle-genomics

How to do inheritance / transmission queries in BigQuery Variant Schema


The Variant Schema used by Google Genomics Variant Transform pipelines represents genotypes as nested records in BigQuery - for example:

1000 Genomes variant examples with 4 genotypes

(from: https://bigquery.cloud.google.com/table/genomics-public-data:1000_genomes.variants?pli=1&tab=preview)

I'm having trouble understanding how to write queries that involve relationships between samples - such as:

select all variants where sampleA.genotype=HET and sampleB.genotype=HET and sampleC.genotype=HOM-ALT

or similar queries where sampleA and sampleB are parents of sampleC and you're looking for variants that follow a particular inheritance pattern.

How are people writing these queries with the nested schema?


Solution

  • I think that would be something like below - have not tested as table is quite expensive - but one run gave zero output meaning that there is no records that meet that specific criteria - but at least you see the logic of how to do such query

    SELECT * EXCEPT(cnt)
    FROM (
        SELECT reference_name,  start, `end`,
            (SELECT COUNT(1) 
                FROM UNNEST(call) 
                WHERE (call_set_name="HG00261" AND genotype[SAFE_OFFSET(0)] = 0 AND genotype[SAFE_OFFSET(1)] = 1)
                OR (call_set_name="HG00593" AND genotype[SAFE_OFFSET(0)] = 1 AND genotype[SAFE_OFFSET(1)] = 0)
                OR (call_set_name="NA12749 " AND genotype[SAFE_OFFSET(0)] = 1 AND genotype[SAFE_OFFSET(1)] = 1)
            ) cnt
        FROM `genomics-public-data.1000_genomes.variants` 
    )
    WHERE cnt = 3