Error in the exported tsv file for GWAS colocalisation

[dbfk2000]

Hi, when I downloaded the exported tsv file for GWAS colocalisation, the file is molQTL colocalisation result. Can you please check this?

[project-defiant]

Dear dbfk2000

Thank you for your question.

The confusion on your query may arise from the fact that the colocalisation analysis is performed in two modes:

1. gwas vs gwas
2. gwas vs molQTL

In your query we can clearly see that there are 5 associated credible sets to the FEV1

When looking at the top rated credible set we can see that it has 70 associations to other GWAS studies

and also has 622 molQTL colocalisations

In case of the downloadable datasets and the depending on your use case, I would recommend querying the joint colocalisation datasets and filtering depending on the rightStudyType value.

This could be equivalent to following SQL query

SELECT 
  leftStudyLocusId, 
  rightStudyLocusId, 
  rightStudyType, 
  colocalisationMethod
FROM (
  SELECT 
    leftStudyLocusId, 
    rightStudyLocusId, 
    rightStudyType, 
    colocalisationMethod
  FROM colocalisation_coloc 
    UNION ALL
  SELECT 
      leftStudyLocusId, 
      rightStudyLocusId, 
      rightStudyType, 
      colocalisationMethod
  FROM colocalisation_ecaviar
)
WHERE rightStudyType = 'gwas';  -- gwas vs gwas
-- WHERE rightStudyType != 'gwas'; -- gwas vs molQTL

I hope this clears your question.

[project-defiant]

The downloadable datasets for colocalisation:

• colocalisation_coloc
• colocalisation_ecaviar

both datasets contain the information about the gwas vs gwas and gwas vs molQTL colocalisations. Have a look at the description on downloads page.