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3. Tutorial
The directory SAFFARI/resources/ includes example files you can use to test and run the fine-mapping pipeline.
The top loci file Mullins_2021_toploci.csv contains the top GWAS loci with genome-wide significance (P < 5 × 10−8), while the file Mullins_2021_loci_ranges.tsv is the output after running the fetch_UKB_LD_names module (i.e., formatted top loci file).
Make sure to also download
(i) the baseline-LF2.2 UKB annotations
(ii) the UKB LD matrices and/or plink bfiles for LD estimation (depending on the LD format of your data) within the resources/ directory.
To ease the running process process, the files/folders shall be named as follows:
(i) baseline-LF2.2 UKB annotations folder as UKBB_priors
(ii) the UKB LD panel as UKBB_LD
(iii) the plink bfiles for LD estimations as genotype_ref_panel
Links to download these files can be found in the Dependency Wiki page. All data were retrieved from Mullins, N., Forstner, A.J., O’Connell, K.S. et al. Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology. Nat Genet 53, 817–829 (2021). Downloaded from the PGC website
Links to download these files can be found in the Wiki page.