Split studies and summary statistics for PMID:30104761

[eks-ebi]

This publication was curated some time ago, and split into 4 studies because associations were only reported in the paper for these 4 studies. However, summary statistics were later obtained manually from Open Targets and added.

Three studies correctly have only the one set of summary statistics matching the trait analysed in that study:

• GCST008371 = thyroid cancer
• GCST008372 = colorectal cancer
• GCST008373 = glaucoma

However, for the remaining study (GCST008370 = coronary artery disease), the FTP folder contains up to 1,403 summary statistics files for many different traits which were also analysed as part of the project. The plan was to split these into separate entries once the deposition app was in production, but this has not yet been done.

Tasks:

• [ ] There is no submission for this publication, so in order to split the studies, the data will first need to be extracted and recurated into a submission template.
• [ ] Upload new metadata
• [ ] Move summary statistics into the correct new folders

[earlEBI]

The original GCSTs will also need to be kept which will require developer time well before a data release is due to start.

[earlEBI]

@ljwh2 I don't think I can find the key anywhere in the paper that explains what each sumstats filename relates to... I found this file online. Do you think I can use this for mapping and for sample case control numbers? https://github.com/opentargets/genetics-sumstat-data/blob/master/extras/prepare_uk_biobank_gwas_catalog/SAIGE/1_stream_to_gcs/manifest/SAIGE_UKBiobank_URL_Nov2017_v3.tsv

Our sumstats files: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST008001-GCST009000/GCST008370/?C=N;O=D

[earlEBI]

PMID is currently closed for submission as it was previously curated through the Curation App. Status needs to be changed to 'open for submission' well before a DR starts, so that I can submit the new studies through the submission app.