Access to ftp json files of Colocalisation analysis

Data Access
1

Hello,

I was wondering where i can find the json files of the colocalisation analysis of OT genetics.

Thank you in advance :slight_smile:

2

Hi,

The colocalization datasets can be downloaded from here: ftp://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d_coloc in parquet format.

The schema of the dataset looks like this:

root
 |-- coloc_n_vars: integer (nullable = true)
 |-- coloc_h0: double (nullable = true)
 |-- coloc_h1: double (nullable = true)
 |-- coloc_h2: double (nullable = true)
 |-- coloc_h3: double (nullable = true)
 |-- coloc_h4: double (nullable = true)
 |-- left_type: string (nullable = true)
 |-- left_study: string (nullable = true)
 |-- left_chrom: string (nullable = true)
 |-- left_pos: integer (nullable = true)
 |-- left_ref: string (nullable = true)
 |-- left_alt: string (nullable = true)
 |-- right_type: string (nullable = true)
 |-- right_study: string (nullable = true)
 |-- right_bio_feature: string (nullable = true)
 |-- right_phenotype: string (nullable = true)
 |-- right_chrom: string (nullable = true)
 |-- right_pos: integer (nullable = true)
 |-- right_ref: string (nullable = true)
 |-- right_alt: string (nullable = true)
 |-- coloc_h4_h3: double (nullable = true)
 |-- coloc_log2_h4_h3: double (nullable = true)
 |-- is_flipped: boolean (nullable = true)
 |-- right_gene_id: string (nullable = true)
 |-- left_var_right_study_beta: double (nullable = true)
 |-- left_var_right_study_se: double (nullable = true)
 |-- left_var_right_study_pval: double (nullable = true)
 |-- left_var_right_isCC: boolean (nullable = true)

As the dataset is specific for colocalization, you might need to join the table with association and study level information stored under https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/v2d/.

Please let us know if there’s anything else we can help with!

Best,
Daniel

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