Harmonizing the studies from PMID: 37156999

EBISPOT / gwas-sumstats-harmoniser

GWAS Summary Statistics Data Harmonisation

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Harmonizing the studies from PMID: 37156999 #100

Open jiyue1214 opened 4 weeks ago

jiyue1214 commented 4 weeks ago

Harmonising the data for PMID:37156999. Data are available here:

jiyue1214 commented 3 weeks ago

Already been formatted and is waiting to be re-harmonised again after maintenance.

Question: For each trait, author provide a EAS and EAS_EUR data. Inside the EAS_EUR data, it has fours sets of beta,p_value and se for meta, EAS, Finnish, and non-Finnish European. EAS data comes from the EAS data.

Finnish data comes from FinnGen, while non-Finnish European comes from PMID: 28067908, which is available in the GWAS catalog already.

Should we split the EAS_EUR or not?

ljwh2 commented 3 weeks ago

@eks-ebi to look into this

eks-ebi commented 3 weeks ago

given that the Finnish and non-Finnish European data are already published elsewhere, I would say we should not split them. Sounds like it's fine to have just two studies for each trait: 1) EAS and 2) EAS_EUR. But I'll have a closer look at the paper now to double check

jiyue1214 commented 3 weeks ago

After discussion, for the EAS_EUR data, we only keep the meta result and remove p_value, beta and se for eas, FIN and non-FIN European to avoid misleading results in the harmonised file.

sajo-ebi commented 1 week ago

Harmonisation not working due to codon maintenance related issues @jiyue1214 is looking into it

jiyue1214 commented 1 week ago

GCST IDs of the study: GCST90446795
GCST90446794
GCST90446793
GCST90446792
GCST90432182
GCST90292538

jiyue1214 commented 1 week ago

@karatugo. Could I ask for your help that these studies were submitted successfully, but I cannot find the file either from depo folder "/hps/nobackup/parkinso/spot/gwas/data/sumstats/depo/staging/" nor staging folder "/nfs/production/parkinso/spot/gwas/prod/data/summary_statistics". (Not on FTP as well) Do you have any suggestions?

karatugo commented 2 days ago

Discussed on Slack, adding here too.

The files were validated successfully on 28/29 Aug but they are not synced to staging FTP (probably due to post-maintenance Celery or scrontab errors). Unfortunately the files are removed from the validation directory, and therefore I suggest them to be submitted again.