nealelab/ukbb_ldsc

Sample code for ldsc analyses in UKBB

UKBB ldsc site

Scripts used for generating the results site for LD score regression (LDSC) analysis of the UK Biobank GWAS produced by the Neale Lab. You can read more about that GWAS effort here and read the hertiabililty analysis post for our initial thoughts on these results.

Contents of the site include:

• Results browser
• Interactive plots
• Extended methods descriptions
• Detailed results pages per phenotype
• Downloads page

Scripts used for the LD Score regression analysis itself are in the UKBB_ldsc_scripts dependency. They've been separated to make it easier for you to pull//fork/otherwise use those scripts without ending up with a download of the whole results site.

Version History

• September 2017: first release
• October 2019: round2 release
• October 2022: minor formatting fixes and link updates (AWS, Pan-UK Biobank)
• May 2023: fix typo in description of effective N on sample size plots page

Main contents of this repo

• ./site_build/build_site.R: main driver script to build the static website using R Markdown. Copies the necessary source files into this directory and updates _site.yml to allow a clean build. Includes options to only generate a subset of the site for easier testing.
• ./docs/: The full contents of the results site hosted on Github Pages.
• ./UKBB_ldsc_scripts/: code for the LDSR analysis, including the Rmd files for results processing that are included in the methods section of this site. See the UKBB_ldsc_scripts repo for full description.
• ./site_source/: source code for building the site, including:
• ./rmd_source/: R markdown source for each page of the site. _h2_part_template.html is used to generate each of the individual phenotype pages, adapting to the results for that phenotype.
• ./yml_source/: yaml code for the structure of the site and the pass parameters for rendering each page. Split into pieces to allow testing rendering subsets of the site. Full site yaml is stitched together by ./site_build/build_site.R at run time.
• analytics_header.html: page header code to count hits and downloads
• ./sandflat and dt_styles.css: custom CSS based on Bootswatch themes and styling options for Datatables
• make_favicon.R and ./icon/: favicon images for browser tabs on various platforms

Credits

Site generated by Raymond Walters (i.e. all mistakes are his), with helpful improvements from Duncan Palmer and support from the full Neale Lab UKB team. See the site for full credits for this project.

For any questions/comments/feedback, email [email protected].

ukbb_ldsc's Issues

Run ldsc locally

Hi,

I am not familiar with google cloud and hope to run the anlaysis locally. Is there a way for me to download the files from Google Cloud? For example, I want to get sumstats files but I don't know how to find gs://ukbb-gwas-results/ldsc/

Reproducibility with ldsc package?

Hi,

I guess this is a bit unusual, but I was wondering how can I use the sumstats provided on UKB Heritability (for instance, I used LDSR-formatted summary statistics data provided here) to run locally (using ldsc tool)?
I initially downloaded summary stats, and fed into ldsc with different LD scores (both partiotioned: 1000G_Phase3_baselineLD_v1.1_ldscores.tgz and for univariate analysis: eur_ref_ld_chr/eur_w_ld_chr), but my intercept (and other stats) were different to those reported online. Am I missing something here? are those summary stats outdated (I guess round 2 is the latest, no?)?

Thanks!
Oveis