OpenGWAS

We built the OpenGWAS resource to be a free and open platform to support work on GWAS summary data. Much of it is based on extensive feedback on @mrbase2 from both internal and external colleagues. Paper here: bit.ly/2DRbHGT, key points below:

12 month training fellowship with opportunities to develop research software engineering and/or drug discovery expertise working with @OpenGwas and @epigraphdb at @mrc_ieu bristol.ac.uk/integrative-ep…

We are recruiting two new posts to join the @OpenGwas team (@mrc_ieu): a research software engineer and a research data officer. bristol.ac.uk/jobs/find/deta… and bristol.ac.uk/jobs/find/deta…

@Eric_Fauman @pietznerm Thanks Eric. Yes underflow is a problem for anything smaller than 1e-300. The smallest P value in the dataset is therefore unclear

@OpenGwas @pietznerm What's the smallest p-value you found? I've been playing with some of your sum stats and so far have found 6e-3567. Unfortunately underflow in your vcf file is reported as "inf" instead of the actual p-value, so the above value is calculated from beta and se

@pietznerm Further details of the GWAS analysis can be found here data.bris.ac.uk/data/dataset/p… Further details on the phenotype preparation can be found on the resources tab at this page on the UKB website, eg. biobank.ndph.ox.ac.uk/showcase/field…

@pietznerm The metabolites were transformed using rank-based inverse normal transformation prior to analyses. We adjusted association analyses by sex, array and fasting time. We used BOLT-LMM (linear mixed model) to account for both relatedness and population stratification

@NPirastu @uk_biobank Yes. You can click through to the downloads here gwas.mrcieu.ac.uk/datasets/?gwas… or use wget #bulk-downloads" target="_blank" rel="nofollow noopener">gwas.mrcieu.ac.uk/about/#bulk-do… Alternatively, packages also available to run post GWAS analyses without downloading the bulk data mrcieu.github.io/gwasglue/

@OpenGwas @uk_biobank Is there a way to download the full summary stats directly?

We GWAS'd the metabolites released by @uk_biobank twitter.com/uk_biobank/sta… and deposited the summary data in Open GWAS gwas.mrcieu.ac.uk. The summary data can be assessed via R (mrcieu.github.io/ieugwasr/) or python (github.com/mrcieu/ieugwas…)

@jschwart37 @uk_biobank Yes you can! You can click through to the metabolite download links here gwas.mrcieu.ac.uk/datasets/?gwas… programmatic access also possible via wget as you already found #bulk-downloads" target="_blank" rel="nofollow noopener">gwas.mrcieu.ac.uk/about/#bulk-do…

@OpenGwas @uk_biobank Also very keen to know if we can get full summary stats for these metabolites!

Also available via @mrbase2 and mrcieu.github.io/TwoSampleMR/ Thank you @uk_biobank, @NgaleHealth , @MCarol_Borges, @elswob and @tomrgaunt

Join me at #ElasticCC where I'll be talking about how we use Elasticsearch for @OpenGwas. This is @Elastic’s free technical event from the community, for the community — happening from Feb 26 - 27 ela.st/community-conf…

Back up and running again!

OpenGWAS currently down due to sever outage with our cloud hosting provider. Apologies to our users. Problem also affecting @mrbase2

The OpenGWAS database, your one-stop-shop for complete #GWAS summary datasets & metadata for the scientific community. Open source, open access, & free for all! Find out more about this phenomenal resource at: biorxiv.org/content/10.110… @mrc_ieu @BristolBRC

Sorry, this is the correct link! gwas.mrcieu.ac.uk/files/ukb-b-19…

QC process - we align the non-effect allele to the human genome reference sequence; and annotate the positions with dbSNP identifiers. Example QC report: gwas.mrcieu.ac.uk/datasets/ukb-b…

We built the OpenGWAS resource to be a free and open platform to support work on GWAS summary data. Much of it is based on extensive feedback on @mrbase2 from both internal and external colleagues. Paper here: bit.ly/2DRbHGT, key points below:

Huge thanks to @The_MRC, @OracleCloud and @wellcometrust for funding much of this, and team (@explodecomputer @tomrgaunt @elswob @matt_s_lyon @prime2 @assetweb @JonJHallett and others) for making a hopefully useful community resource

Continued data harvesting - for new GWAS results that are published, upload them to the EBI GWAS catalog and we will pull them in from there. For unpublished results, or large batches, we have pipelines to do that. Get in touch here: github.com/mrcieu/opengwa…